I have a script that loops through and opens a file, edits it, exports it and then reverts and does it again for x number of pages. The script used to work fine when manually enabling and disabling fonts but not we have had a few font issues in the PDFs and we're thinking it has to to with the auto-activation interrupting the script or something like that.
Since the file is opened manually the first time that would allow the auto activation to occur once. The script would then run and disable it, do all the edits. exports. and reverts and then when its done enable auto-activation again.
Let me know if you have any ideas or if you happen to already know the about the issue.