I had the weirdest thing happening. I was diffing some .java files, and one side was totally blank. If I switched the diff rule from "Java Source Tidied" to ordinary "Java Source" then it worked.

The problem was that jalopy (called by CLASS_to_JAVA_tidied.bat) was too old to deal with some new Java syntax, and was simply erroring out with a stack trace. Updating to a newer jalopy (0.1-1.5rc3 seems to work fine) fixed it, but I have a suggestion:

Have a way to detect and possibly report errors coming from an external program used in a diff. Maybe look for stderr output, or a non-zero process return, not sure. Maybe have an option to decide what is considered an error case.

Otherwise it's confusing as to what is really going on when a file shows up blank.