Thank you very much.
Yes it was only on fullscreen and unredir-if-possible = false; option fixed the issue.
I also saw a vsync option there and tried to turn it on with vsync = true; but it only caused picom to crash so had to disable it again.
Generally speaking, as an out of the box experience I still feel like Manjaro i3 edition was more ready to use comparing to Bspwm edition, though this was probably because I ran into some issues after the fresh installation. However I found Bspwm more snappy and easier to use. Since the issues are fixed now I think I can slowly start ricing. 
Thanks again and hope you have a nice day.