Issue resolved - but a question remains...

What I did was open a backup of my wallet with blockchain.info. It still showed my balance at zero... so I exported that blockchain wallet to Multibit, which did show a balance - so sent that balance to another system, yay!

Now, I have the same wallet keys and transaction history being displayed in all MultiBit, Blockchain, and Bitcoin-QT... can that be an issue? Do I need to move everything back to Bitcoin-QT (which is still showing that unconfirmed transaction)?