I have the exact same problem. LimeWire crapped out while trying to upgrade to 4.6.

I have:

Uninstalled
deleted .limewire folder
Updated Java to 1.5
set javaw.exe and limewire.exe to full access in firewall
Made sure port 6346 was forwarded to computer running limewire

None of this has helped. It still hangs up there. I cannot even kill the task or restart computer. I have to reset the computer manually.