I rarely use Diffzilla via SE except via version control menu (way too much point and click work to get it set up when I can just type the parameters on the command line).
However, I went through the dialogue set up to diff from within SE of the two files (not directories) and it worked properly. Checking all the other means I had already tried (git difftool, vsdiff, and version control diff against most up to date), now appear to work correctly. So I wondered if there was some configuration with the new beta that wasn't set that was triggered on the first time executed via SE.
On this hunch, I restored my old 20.0.3 installation (~/slickedit & ~/.slickedit). Reinstalled beta3 on top of my installation and reproduced the problem the first time (running vsdiff from the command line). So it *appears* that if you don't run Diffzilla from within SE via the File Difference menu at least once, it will always jump to the end of the file. Note, as I mentioned in prior posts, that running Diffzilla via Version Control -> <whatever> reproduces this problem as well. It appears to clear up specifically after launching it via File Difference.