Thanks for bringing this up, I've often meant to but never got around
to actually doing so. I often experience this same phenomenon.
Also, I save as binary, not text, as "foo.pat". Also, I'm not sure
if the result I get is "foo35.pat" or "foo.pat35" - it hasn't
happened in the last few days, and I don't have any remaining
examples of those files to look at.
Also, for further specification of the problem, it appears as though
the "foo.pat" file *does* have the saved changes in it - my guess is
that the "foo35.pat" type files are just temp files that for some
reason are not disposed of properly upon patcher saving...