I did not.
I painfully went through the menu within SE to traverse and find the two files I wanted to diff and had no problem running Diffzilla from within SE. I noticed in the command line usage that Diffzilla now has a means of launching the dialog from the command line as well as mentioning passing an SE config file, so I suspect that this addition now causes locking issues.
I take that back, I have been playing with the Vitual Memory/Cache tweaks discussed in another thread between jporkkahtc and Clark, but I wouldn't expect this to impact this issue.