When you're wide, it's much much more difficult to bring prices back to normal (as notthatamanda's headache will attest). I've gone 10 days contacting Amazon by phone 3-4x trying to return a book to its normal price. I made a post here once about that. One of the members on writersanctum said they contact Amazon every time they try to return their book to normal price. In my experience, I've had to contact them direct only about 50% of the time.
The only trick I can suggest is that if you run a promotion, bring the price back to normal on Amazon last. Return all the other retailers first, then wait 12 hrs or even a day.
I'm so used to this problem that I'm actually planning a promo where I'm running an extra promo day for Amazon only on the last day. That way I can patiently wait a day to return the book on Amazon to normal price while, hopefully, selling more books through Amazon (of course, the promo on the last day advertises to Amazon only). I'll let you know if the book still gets stuck at 99c (probably will, right?).
As far as paperbacks, my paperbacks have sold for as low as $4 from price matching. That used to bother me, but Amazon will match your price for paperbacks. So, if people buy a ton of low priced books, the only one losing money there is Zon. If you sell a ton when discounted and your royalty's higher, they'll raise it back up I'm sure ;)