Re: non root user resolution settings reverting to default.
X always uses xorg.conf to determine which configuration to use (including the modes). If you're going to runlevel 5, then its almost certainly using /etc/X11/xorg.conf (unless you've intentionally hacked it to do otherwise).
I suspect that whichever window manager you're using is trying to be clever and changing to a different mode per some user-specific configuration change you've mode (and potentially forgotten about).
Is this problem specific to all non-root users, or just 1?