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...
Okay, I was faster, than community

Found the solution by myself.
1. In the wallet Go to Help -> Debug window -> console
2. In th console issue "checkwallet" command. In the output you should see the amount of your lost coins.
3. Issue the "repairwallet" command. Don't afraid, that nothing happens - the wallet is working, and soon you will see your lost coins on the account.
4. After you've got your coins back, again check the wallet. You should see {"wallet check passed" : true} if all is ok.
Your ability to improvise logically will stand you in good stead! Thank you also for sharing your problem solving. May I include your work in the DMD FAQ?