Once it's corrupt like this the emplode config.ini editor seems to keep messing up.

Correct. Once the config.ini has become corrupted, the Emplode config.ini editor will not work on it and the only resolution is to delete it and start over (hopefully with a new copy containing the data from the corrupted one).

Some of the extra junk added to my config.ini appeared to be from other files on the empeg. Quite weird.

This is scary, because that sounds like cross-linked sectors or something.

Empeg guys, are you reading this?