Same problem here, I have Vista x64 SP2 and I never touched the default vsync .ini settings.
Some days ago the change-day was at 11:06 PM and now it's 04:20 AM. I have about 40 hours of gameplay, what can I do? I don't think that Bethesda can fix it.
bcdedit command doesn't works. I have tested the ratio between QueryPerformanceCounter and GetTickCount (with WinTimerTester 1.1) and it's correct (1.0000, perfect) so useplatformclock (in my case) is useless and unnecessary.
I would try "set gamehour to 0" command, but I don't understand when i have to use it. When the day have to change (suppose 12:00 AM) or When the day change actually (04:20 AM)?.
I don't think it matters about just V-Sync being disabled or enabled. What I believe matters is that the frame rate stays below 60fps. Your frames per second may be influenced by the fact that you have a great system, and a great monitor to boot. Most monitors run at 60 - 75Hz. Higher end monitors do up to 120Hz or even higher. If v-sync is enabled and your gfx cards are able to pump out good fps, that means your system is running the game faster than intended. This gets to be visible when your physics in game go wonky. If you have odd stuff happening like stuff on tables bouncing around, or creatures/characters you kill bouncing around like crazy, could be an indicator that your system is running TOO good. If fps get limited to 60, then it SHOULD keep your game's clock and physics running properly. At least that's what I'm guessing.
I've put in over 100+ hours on one character and am working on my 2nd character now and have not had this issue. But my fps RARELY ever hit 60. Most of the time I'm around 35-45. Maybe running Fraps at the same time using the graphic overlay fps counter might help you track down the issue? I know that there's also a console command in Elder Scrolls that allows you to see your FPS, but I don't know what it is at the top of my head.
In response to your question on when to run it. I believe you have to run the command at 00:00 in game time.