bitcoin-qt stops subsequent RPC calls, then won't shut down
I was having a different somewhat related problem and stumbled across this thread. It seems that bitcoin-qt creates a .lock file to make sure no other program is using the same folder. If the app crashes, the lock file might not be deleted which could cause it to throw up an error about the program already being open. The .lock file is hidden, though, so you won't see it unless you have hidden files turned on. Deleting the .lock file might fix this for you.