Each of the nodes I connect to have been modified to hold hundreds of connections. Likewise, I've tried restarting without connecting to them, rescanning, etc... If it's a matter of starting it differently, rescanning, or redownloading the block chain, you can assume I have already tried it.
Ok, let's eliminate some possible problems.
Have you tried using your existing wallet.dat with the stock client (v0.6.2) that connects to peers (using the default manner)?