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I spent some time looking into ways that you could troubleshoot this. I opened process monitor
and watched for explorer to update this key...
...but alas, that did not happen. Mine was a simple test: move a desktop shortcut and then press F5. Explorer writes to that key in XP - but I did not see that happen in Windows 7 (maybe I missed it). Anyway, my hope was to be able to tell you how to setup and filter process monitor's data in a way that would capture whatever app was barfing your desktop shortcut's positions.
All I can suggest at this point is to use an app like Ztruker suggested - I use Desktop Restore
If you ever figure what causes this - please post your info here :-)