Almost exactly the same thing has happened to me.
I guess I will have to wait until they release a half way decent client, then I will get my ETH back.
You do realise that you don't need a fully synced wallet to spend you ETH?
yeh i know, i've got 0.8.7 running on one pc and 0.8.6 running on another and neither of them ever sync, they've been running for a week almost now and always 1000 blocks behind or more. Neither of them see my ETH balance either.
I log into My Ether wallet, import my keystore file and bang, my full balance is there. I've transferred it out to a Jaxx wallet now and backed it all up. Ethererum wallet/Mist can get stuffed, not wasting my time with their wallets any more.