I do also have similiar issues running seamless mode in fluxbox as you do, but not exacly...
when i move windows in the virtual machine all windows opend in fluxbox will start flickering, it looks like some refresh is being made.
I get flickering windows as well when I move windows and open windows etc in seamless mode. Fluxbox here also....Debian Sid Kernel 2.6.22, virtualbox 1.5.2
So then it's a fluxbox related issue?, maybe we should consider filing a bug report to the fluxbox devs?.
btw broli2 said that he didn't get the issue and said it could be a vidcar issue, i guess he mean video card.
So if we post our fluxbox version + video drivers it might help.
System: Gentoo Linux 2007.1 - AMD64
Fluxbox version: Fluxbox 1.0.0-gentoo
Video Drivers: Nvidia 100.14.19
Don't think it would be videocard related since I tried a few other wms including dwm and and openbox and had no such issues. Perhaps disabling certain compile time options will fix the issue? Not sure, I don't have time to fiddle with it to much really. BTW I am just using plain old NV driver in xorg...I have an old tnt2 card.
We're up to VirtualBox 3.0.0 and I'm still encountering this issue. My VirtualBox also cannot render Full Screen properly as shown in the screenshots. I think that's what's causing my seamless mode to go out of wack.
Fullscreen Mode (with conky killed):
Fullscreen Mode (sometimes it gets a little further and ends up like this):
Seamless Mode (I'm guessing that because fullscreen mode is crazy, the problem overflows into seamless for this):