Error on boot: invalid sector size 65535

My setup:
Manjaro version 5.15.50-1, installed with LUKS encryption
CPU: Intel Core i5-10600
Motherboard: MSI B460M-Pro-VDH
Primary SSD: Western Digital Black SN750 1TB M.2-2280 (WDS100T3X0C-00SJG0)

This is not a dual boot GRUB setup. I have Windows on a completely separate SSD and I switch between the two by changing the boot order in the BIOS. There are 3 drives installed in the case: the primary SSD with Manjaro, the secondary SSD (SanDisk SDSSDHII120G) with Windows, and a third (WDC WD3200AAKS spinning disk, not SSD) with data. There is also a 4th portable drive plugged into a USB port for backups (WD My Passport 2626).

When I boot up, I see an error message

error: invalid sector size 65535.

followed by the normal prompt for the decryption master key

Attempting to decrypt master key…
Enter passphrase for hd5,gpt2 (long-code-here):

I also have exactly (to the extent humanly possible) the same installation of Manjaro on a laptop, and do not see this error message. The hardware is completely different but the process I followed to install Manjaro was the same, from the same flash drive.

I’m not seeing any ill effects, but I’m curious what that error means.

I saw a related post, so here are the logs requested there:

> inxi -Fza
  Kernel: 5.15.50-1-MANJARO arch: x86_64 bits: 64 compiler: gcc v: 12.1.0
    parameters: BOOT_IMAGE=/boot/vmlinuz-5.15-x86_64
    root=UUID=f65c7da7-e33a-4a85-8192-eb4496c4ca9a rw quiet
    root=/dev/mapper/luks-605a72eb-231c-4f8f-8bed-60a8a0e0bfa7 splash
    apparmor=1 security=apparmor
  Desktop: GNOME v: 42.2 tk: GTK v: 3.24.34 wm: gnome-shell dm: GDM v: 42.0
    Distro: Manjaro Linux base: Arch Linux
  Type: Desktop Mobo: Micro-Star model: B460M PRO-VDH (MS-7C83) v: 1.0
    serial: <superuser required> UEFI: American Megatrends v: 1.40
    date: 12/04/2020
  Info: model: Intel Core i5-10600 bits: 64 type: MT MCP arch: Comet Lake
    gen: core 10 built: 2020 process: Intel 14nm family: 6 model-id: 0xA5 (165)
    stepping: 3 microcode: 0xF0
  Topology: cpus: 1x cores: 6 tpc: 2 threads: 12 smt: enabled cache:
    L1: 384 KiB desc: d-6x32 KiB; i-6x32 KiB L2: 1.5 MiB desc: 6x256 KiB
    L3: 12 MiB desc: 1x12 MiB
  Speed (MHz): avg: 800 min/max: 800/4800 scaling: driver: intel_pstate
    governor: powersave cores: 1: 800 2: 800 3: 800 4: 800 5: 800 6: 800 7: 800
    8: 800 9: 800 10: 800 11: 800 12: 800 bogomips: 79235
  Flags: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
  Type: itlb_multihit status: KVM: VMX disabled
  Type: l1tf status: Not affected
  Type: mds status: Not affected
  Type: meltdown status: Not affected
  Type: mmio_stale_data mitigation: Clear CPU buffers; SMT vulnerable
  Type: spec_store_bypass
    mitigation: Speculative Store Bypass disabled via prctl and seccomp
  Type: spectre_v1
    mitigation: usercopy/swapgs barriers and __user pointer sanitization
  Type: spectre_v2 status: Vulnerable: eIBRS with unprivileged eBPF
  Type: srbds mitigation: Microcode
  Type: tsx_async_abort status: Not affected
  Device-1: Intel CometLake-S GT2 [UHD Graphics 630] vendor: Micro-Star MSI
    driver: i915 v: kernel arch: Gen9.5 process: Intel 14nm built: 2016-20
    ports: active: DP-1 empty: HDMI-A-1,HDMI-A-2,HDMI-A-3 bus-ID: 00:02.0
    chip-ID: 8086:9bc8 class-ID: 0300
  Device-2: Sunplus Innovation FHD Camera Microphone type: USB
    driver: snd-usb-audio,uvcvideo bus-ID: 1-3.1.4:8 chip-ID: 1bcf:28c4
    class-ID: 0102 serial: <filter>
  Display: wayland server: v: with: Xwayland v: 22.1.2
    compositor: gnome-shell driver: N/A display-ID: 0
  Monitor-1: DP-1 res: 1920x1080 size: N/A modes: N/A
  OpenGL: renderer: Mesa Intel UHD Graphics 630 (CML GT2)
    v: 4.6 Mesa 22.1.2 direct render: Yes
  Device-1: Intel Comet Lake PCH-V cAVS vendor: Micro-Star MSI
    driver: snd_hda_intel v: kernel bus-ID: 1-10:10
    alternate: snd_sof_pci_intel_cnl chip-ID: 0c76:120f class-ID: 0300
    bus-ID: 00:1f.3 chip-ID: 8086:a3f0 serial: <filter> class-ID: 0403
  Device-2: JMTek LLC. MICUSB type: USB
    driver: hid-generic,snd-usb-audio,usbhid
  Device-3: Sunplus Innovation FHD Camera Microphone type: USB
    driver: snd-usb-audio,uvcvideo bus-ID: 1-3.1.4:8 chip-ID: 1bcf:28c4
    class-ID: 0102 serial: <filter>
  Sound Server-1: ALSA v: k5.15.50-1-MANJARO running: yes
  Sound Server-2: JACK v: 1.9.21 running: no
  Sound Server-3: PulseAudio v: 16.1 running: yes
  Sound Server-4: PipeWire v: 0.3.52 running: yes
  Device-1: Realtek RTL8111/8168/8411 PCI Express Gigabit Ethernet
    vendor: Micro-Star MSI driver: r8169 v: kernel pcie: gen: 1 speed: 2.5 GT/s
    lanes: 1 port: 3000 bus-ID: 02:00.0 chip-ID: 10ec:8168 class-ID: 0200
  IF: enp2s0 state: up speed: 1000 Mbps duplex: full mac: <filter>
  IF-ID-1: tun0 state: unknown speed: 10 Mbps duplex: full mac: N/A
  Device-1: Cambridge Silicon Radio Bluetooth Dongle (HCI mode) type: USB
    driver: btusb v: 0.8 bus-ID: 1-3.1.3:6 chip-ID: 0a12:0001 class-ID: e001
  Report: rfkill ID: hci0 rfk-id: 0 state: up address: see --recommends
  Local Storage: total: 3.13 TiB used: 322.43 GiB (10.1%)
  SMART Message: Unable to run smartctl. Root privileges required.
  ID-1: /dev/nvme0n1 maj-min: 259:0 vendor: Western Digital
    model: WDS100T3X0C-00SJG0 size: 931.51 GiB block-size: physical: 512 B
    logical: 512 B speed: 31.6 Gb/s lanes: 4 type: SSD serial: <filter>
    rev: 111110WD temp: 41.9 C scheme: GPT
  ID-2: /dev/sda maj-min: 8:0 vendor: SanDisk model: SDSSDHII120G
    size: 111.79 GiB block-size: physical: 512 B logical: 512 B speed: 6.0 Gb/s
    type: SSD serial: <filter> rev: 00RL scheme: GPT
  ID-3: /dev/sdb maj-min: 8:16 vendor: Western Digital
    model: WD3200AAKS-00L9A0 size: 298.09 GiB block-size: physical: 512 B
    logical: 512 B speed: 3.0 Gb/s type: N/A serial: <filter> rev: 3E01
    scheme: MBR
  ID-4: /dev/sdc maj-min: 8:32 type: USB vendor: Western Digital
    model: WD My Passport 2626 size: 1.82 TiB block-size: physical: 512 B
    logical: 512 B type: N/A serial: <filter> rev: 1028 scheme: MBR
  ID-1: / raw-size: 914.17 GiB size: 898.75 GiB (98.31%)
    used: 45.32 GiB (5.0%) fs: ext4 dev: /dev/dm-0 maj-min: 254:0
    mapped: luks-605a72eb-231c-4f8f-8bed-60a8a0e0bfa7
  ID-2: /boot/efi raw-size: 300 MiB size: 299.4 MiB (99.80%)
    used: 440 KiB (0.1%) fs: vfat dev: /dev/nvme0n1p1 maj-min: 259:1
  Kernel: swappiness: 10 (default 60) cache-pressure: 100 (default)
  ID-1: swap-1 type: partition size: 17.04 GiB used: 1.8 MiB (0.0%)
    priority: -2 dev: /dev/dm-1 maj-min: 254:1
    mapped: luks-8043e7b1-f723-4004-92c2-696f3a875ae6
  System Temperatures: cpu: 40.0 C mobo: N/A
  Fan Speeds (RPM): N/A
  Processes: 378 Uptime: 5h 26m wakeups: 0 Memory: 15.49 GiB
  used: 6.43 GiB (41.5%) Init: systemd v: 251 default: graphical
  tool: systemctl Compilers: gcc: 12.1.0 clang: 13.0.1 Packages: pacman: 1511
  lib: 436 flatpak: 0 Shell: Zsh v: 5.9 running-in: gnome-terminal
  inxi: 3.3.19


> sudo parted -l
Model: ATA SanDisk SDSSDHII (scsi)
Disk /dev/sda: 120GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt
Disk Flags: 

Number  Start   End    Size   File system  Name  Flags
 1      1049kB  368MB  367MB  fat32              boot, esp
 2      368MB   119GB  118GB  ntfs               msftdata
 3      119GB   120GB  910MB  ntfs               hidden, diag

Model: ATA WDC WD3200AAKS-0 (scsi)
Disk /dev/sdb: 320GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos
Disk Flags: 

Number  Start   End    Size   Type     File system  Flags
 1      1049kB  106MB  105MB  primary  ntfs         boot
 2      106MB   320GB  320GB  primary  ntfs

Model: WD My Passport 2626 (scsi)
Disk /dev/sdc: 2000GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos
Disk Flags: 

Number  Start   End     Size    Type     File system  Flags
 1      1049kB  2000GB  2000GB  primary  ntfs

Model: WDS100T3X0C-00SJG0 (nvme)
Disk /dev/nvme0n1: 1000GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt
Disk Flags: 

Number  Start   End     Size    File system  Name  Flags
 1      2097kB  317MB   315MB   fat32              boot, esp
 2      317MB   982GB   982GB                root
 3      982GB   1000GB  18.3GB

Unplug it and you will not have that error prompt anymore.
That means, since is an NTFS partition on it, whatever you have to do to fix the partition or check the disk has to be done from Windows.

@bogdancovaciu Thanks! I was so focused on the problem being with the oldest drive (#3 - the WDC spinning disk) that I did not try to remove the portable drive until you suggested it. You were 100% correct - I formatted with NTFS because I expected to use it only with Windows at the time I set it up.

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