I know with the installer it doesn't actually select 1280x1024 its some other resolution and if your not careful and choose a similar but different res that can throw things out of wack.
Another thing that can and cannot throw things out is the fullscreen mode... are those that are having problems running full screen or are they in windowed mode. It could even be something like different frequency settings from desktop to game .. some games don't like change the frequency say from 85hz on the desktop to 75hz on the game .. or 60hz (default on LCD's) to something higher .. that can change the screen size some and thus affect the position (now this last statement is hypothetical not sure if its possible but stranger things haven been know to happen) Another issue in theory could be the changes of resolutions .. if going from say 1024x768 to 1152x864 that change can affect the game in different ways.. I've had it happen to me all the time with EQ1 before I kept thing the same.
Or we can blame Sony for yet another undocument feature
Hope this helps some out there.