I am running UTC 6.0.0 on a mac with OS X El Capitan and I have activated many fonts permanently only to find them closed again a day or two later. What could be causing this to happen?
Depending on the fonts that are activated, you may be having an issue with duplicate fonts that are active by the system itself.
One suggestion would be to disable FontBook from activating fonts:
If the above suggestion does not resolve your issue, I would suggest contacting our Technical Support team to further assist in diagnosing the issue.
Technical Support: https://www.extensis.com/company/contact-us/
Monday thru Friday 8AM - 4PM PST