I've encountered this bug on the C3200 as well using 5.3.5 full.
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Does the keyboard still work (Menu key -> Menu / "Reboot" possible etc.)?
Yesterday I found a way to reproduce that (or maybe only a similar) problem.
I have created a shellscript-based backup application for weeXpc. That shell script uses the "script" utility for logging the script output.
When this applicatoin is started from a terminal (mrxvt) it works nicely.
However, when it is started directly from the menu using a .desktop file which simply invokes the shell script, the entire GUI isn't responsive anymore: No touch screen input, no keyboard input, and no screen output updates anymore.
However, the system is still operable remotely via ssh.
It seems that the script ustility causes that behavior, because other shell scripts, which are programmed very similar, but without using the script utility, work flawlessly when run from the menu.
And when I change the exec line in the desktop file from
exec=weexpc-backup.sh
to
exec=mrxvt -ip 0 -e "weexpc-backup.sh"
it also works without a problem.
This may not be the same use case as in your cases, but it could be a hint about what causes that problem in general. Maybe someone more knowledgable about X can estimate from these data points, where the root of the problem may be.
Do you have any way ro reproduce the problem on pdaXii13?
daniel