If anyone could help me out, or explain what exactly happened I would greatly appreciate it.
Well, what happened was that someone somewhere cheated you by sending you funds that might have confirmed but then were later double spent. During the period of time while the transaction you received had one confirmation you then unknowingly ended up propagating this cheat to some else (SatoshiDICE) by sending a payment with funds that will never confirm and included a double spent coin.
This transaction back in your history that had cheated you probably came to you from SatoshiDICE. And if true, then prior to that the funds to them were sent by someone trying to cheat SatoshiDICE. So SatoshiDICE had no intention to cheat, but they didn't take proper precautions from sending the "potentially bogus" payout to you.
When they do that (and it is too bad they won't take the actions that would cause their service to stop doing this to people), what they end up doing is having to fix the problem at a later time by sending out a replacement payout. The later replacement payout confirms just fine.
Now you are affected by this negatively because the Bitcoin-Qt client does not handle this condition where a transaction has at least one confirmation and is used in a payment but then at a later time that confirmation vanishes as the result of being double spent against.
This situation where a transaction has at least one confirmation and at a later time ends up being a double spend is something that occurs rarely. For this reason, supporting this condition in the Bitcoin-Qt/bitcoind client has not been a feature that has made it into a release just yet.
Its not the end of the wold but about 3BT basically vanished.
No, they didn't vanish they simply are stuck in transactions that the client doesn't know how to handle as far as canceling after a certain period of time.
So remedies at this point are:
1.) Use joric's fork of pywallet and remove all transactions. Then -rescan.
2.) Create a hybrid EWallet from your wallet.dat. Use
https://blockchain.info/wallet/import-wallet 3.) Export your keys, then create a new wallet and import the keys into the new wallet.