Brainstorm Script keeps reinstalling CAT12

Yes, that could be reason, as it would try to upload to the 'latest' (as it cannot check what is the current number for latest) regardless of what is installed.

Can you manually update the URL in bst_check_internet from:
http://neuroimage.usc.edu/bst/getversion.php
to
https://neuroimage.usc.edu/bst/getversion.php

Then restart Brainstorm and try to install CAT12