You have my sympathy. I recently upgraded (from a really, really, old version) and was disappointed with the 2-second delay on launching DIFF, old version was instant. Also, DIFF failed to highlight differences in some circumstances; it correctly detected files that had a difference, but then would not show those particular differences. So I too was disappointed, relative to my previous experience, but the whole of the rest of the editor is like night-and-day compared to the old one, and the time to search whole folder structures of files is significantly quicker (so much so that at times I don't believe it actually did it!)
Longshot: a fix is coming in HotFix for my problem, but as a workaround they asked me to increase the Wrap Line Length (File options : Load); I increased mine to the MAX value permitted . I had some really long lines in the files that I was trying to DIFF, but my interaction with COBOL was on 80 column punch-cards, so I'm doubting that you have mega-long-lines
I would also make sure that SOURCE DIFF is off (in DIFFzilla OPTIONS)
Perhaps try renaming the file extension and DIFF'ing, in case trying to DIFF that particular file-extension is triggering the crash.