What version you running mid? 8.0?
The scan time schedule SHOULD run off of your system clock, but it is possible that it runs off of the BIOS clock instead...I'm not positive which one it uses. Is your BIOS clock set to GMT by chance? If so, try setting it to your local time/date and adjust Windows time/date accordingly.
Also in the scan schedule, check to see that the 'run on startup if last task was missed' checkbox is unchecked.
Sometimes this will throw a monkey-wrench in the works. That option always threw my Norton Systemworks scheduler off big time...it would start tasks randomly, not always right on startup but when the computer had enough free idle time to think it was time to do the deed.
Also set the scan process priority to high or fast instead of automatic. This won't affect the timing, but it will run the scan through a bit faster when it's going.
Knock on wood, I haven't had any problems with 8.0 except that it uses quite a bit more resources than 7.5 did.
I still use 7.5 on my Linux rigs...no v8.0 for the Linux version yet and it doesn't look like there will be one.