Does it specify the location of where it is scanning? Maybe there is something about that location that your security software isn't able to proceed from.
I would recommend that you put an end to the scan. Force the program to close if you have to, and it doesn't respond for several minutes when you request it to stop. Then get it to scan your computer again, which hopefully it will complete successfully. Personally, I think you should just let the thing run overnight so that there is more than enough time for it to complete.
Also... what program are you using?