Same issue here. Got a ticket opened with them regarding Custom Field issues. This was supposed to be a fix, and it went and caused this problem.
Only way we found to get around it, is to enable the custom fields in the Communication View in the template. And put in the values from there instead of the Custom Fields tab. That seems to work with simple text fields, but doesn't seem to save values from drop-down lists.
Its become a huge headache where on some brands, we had to disable them completely just to be able to process tickets.