Actually, in fact. We are. We started using No-IP for the server. Now that I think about it, the issues didn't really start until after that. We could try reverting to not using it and see how it goes.
Also encountering this issue. It seems to occur randomly and causes some bizarre effects. Select players inventories getting rolled back, small island sized areas rolling back several hours (Any chunks outside of the affected remain completely normal).
The server is currently running LeafDropper, iCurrency, and Realms for mods. We -think- it might be LeafDropper causing it. Started happening sometime after we installed it we think. Will post results after we've had it disabled for awhile.
Here's a bit of what we're seeing when it happens.
2010-12-17 01:25:41 [SEVERE] Unexpected exception
at java.util.AbstractList$Itr.checkForComodification(Unknown Source)
at java.util.AbstractList$Itr.next(Unknown Source)
at java.util.AbstractCollection.removeAll(Unknown Source)