Thanks so much for your comment!! It really gives me peace of mind :)
Try not to worry too much about provera and pregnancy. Provera is a progesterone supplement, and although there are "warnings" about progesterone use in pregnancy, it is a very common supplement to take while pregnant to help aid your body's own progesterone levels. Should you find out that you are in fact pregnant, however, just stop the supplement and ask your doctor whether or not you need additional progesterne. If you do, you would most probably get a different kind, since Provera is usually prescribed to regulate your cycle...especially if you don't ovulate on your own...and not as a supplement in pregnancy.
As for when to take it, I would tend to agree with your gynecologist, that you should take it starting around day 15 of your cycle, but I also don't think it would be that bad if you took it at the same time each month...it would probably just extent your cycles by a few days in months that are longer than 28 days (so in February, for example, it shouldn't even matter).
Best of luck with everything!