Well, from the possibly-useless-suggestion department, have a look at MLDBM::Sync. Granted, it's not behind IO::All's madcap fanciness, but you could have look at how it does it. And then write IO::All::MLDBM::Sync :-)

Or if nothing else, you could make a small test case using MLDBM::Sync directly, leaving out IO::All, and confirm that your problem is within IO::All::MLDBM. But you were probably already thinking that.

Good luck!