I am not sure what I did wrong here. Its kinda strange how I got myself in this position, but I'll try to explain what I did. I had a virtual machine with two wallet.dat files on it. I would use one of them and if I wanted to use the other I would rename wallet.dat to wallet1.dat and then rename the other one wallet.dat and then relaunch bitcoin. In that way I could switch between wallets. Probably not the most efficient way, but that is what I was doing. Anyway, that virtual machine died and I had to spend several hours messing around to get those two wallet files off of it.
I finally do though and I copy them into another machine that had no coins. I delete the existing wallet.dat file (that had no coins) and I relaunch the bitcoin client, which generates a new wallet.dat and recieving address. I copy that address out and put it into a text file. I close down bitcoin client and then I rename wallet.dat to wallet-new.dat and then rename one of the wallets recovered off of the virtual machine to wallet.dat and launch the client again. I then send coins from that wallet to the address I copied into text file. Then I do the same with the other wallet. When I rename wallet-new.dat back to wallet.dat and launch bitcoin again, there are no coins.
If I search for my recieving address on blockchain.info it shows my two transactions and it shows no coins leaving the wallet, but my client still shows it as being empty. I'm worried that I have lost all these coins. Any ideas on what I should try?
If blockchain.info shows that the receiving address has the coins, and you have the wallet to that address, your coins is safe. Have your client finish downloading the blockchain yet?