When you use a fee of 0.0001, every other transaction that offers a miner 0.0005 to solve will get processed before yours.
Some miners won't even bother with a fee of 0.0001.
I've never had a problem with a fee of 0.0001. It may take a few hours to get a few confirmations, but not days.
Since the transactions aren't visible on the network, it would seem that your BTC are still in your wallet, but your Bitcoin-QT is just out of sync somehow.
What I would do is make a backup of your wallet.dat first, then delete all of the files and folders in your Bitcoin-QT data folder except wallet.dat. Restart QT, and it will resynchronize the blockchain, and it should return your coins.
If that doesn't work, you may have to export the private keys from your wallet, and re-import them into a new wallet. I don't know if that would help or not.