I just went through the same thing, and had to run the wallet from the command line with the -rescan option to recover the coins.
Tried this on the synced bootstrap DB - no result

Now, downloading full blockchain, will try on it, but I think this will take some time... Anyway, thank you for advice.
Full blockchain - no result

Dear DMD community, help... Please...
Do not fear, your coins are not lost, the team is simply having a few remaining issues with the wallet, that I'm certain they will work out. I think that making sure you have the addnodes in your conf that I posted a few pages back, will help you to fix the issue.
You haven't lost any coin, so don't worry. Add the addnodes, then let the chain download, or download the chain from the link posted a few pages back as well, then let it sync up and you'll be fine.
I'm certain the next release of the wallet will work out these little kinks and everything will be fine. No worries!