I think I have a similar problem. My wallets sync and check correctly, all transactions show, total balances are ok, but when I open wallet properties I only see a couple addresses which balances don't add up to the wallets' total.
I panicked when I thought I screwed up something with my backup and lost a lot of coins. But it seems they are still there, just hidden somehow.
It's of course 0.94.1, fresh install, doesn't matter if expert mode or not. Restarting doesn't help. I just can't see my change addresses anywhere, except for the Coin Control UI when I want to Send coins. So no more panic.
But it's still an annoyance.
In Wallet Properties there's that tick box "Hide change", but ticking or unticking it does nothing. Is it a known bug or a feature?