I run on a flat panel with a DVI and it's always rock-solid, but I recall at my last job a number of the workstations we had needed to have the refresh rate set in XF86Config so that there was only one choice, 60hz.
From messing around with running Linux on arcade monitors (no, really!) I can tell you that the image not being centered like that is quite likely a timing issue. Running xvidtune will help you create your exact modeline, and strangely enough so will AdvanceMame video setup program. Once you have that modeline in for your desktop resolution, it should always work.
A second complication I had that was similar was with my laptop- it supports a key combination to use the external display, which is somewhat confusion to X. Basically, you had to start it either on the local, on the secondary, or on both displays. Setting it to external only would result in it sometimes "Remembering" the higher refresh rate, causing my display to go off to the right of the screen just like you describe!
SO my advice is to try to make sure your XF86Config *only* allows the correct refresh rate, and make it be one that you have centered as best you can using xvidtune or AdvanceMame's video mode generator.
DB