Hi Brian- In trying to respond to your post I figured out part of what is going on and have been troubleshooting a bit. When I tried to scrub out some comments from a transcription because of the sensitivity of some of that information I realized it stopped giving me the warning.
Basically, if I open a file in CLAN that is giving me the warning and I edit it manually and save the edits through CLAN, the saved file will not produce the font warning even though I did nothing to the headers. This then allows the program to go through the full check procedure ("CLAN Deletion" attached file). If I change the file extension instead to .txt and edit the same information out using a text editor, then change the file back to a .cha file, the file produces the font warning on a check ("Text Editor Deletion" attached file). All of the edits I've done to the files to this point have been through the command box without opening/saving individual files, so that editing seems to be akin to what is happening when I edit using a text editor. That is, the files continue to trip the header warning no matter how many changes I make with the command box.
As I said, adding the "@UTF8 @PID: 11312/c-00012165-1" line in before I imported fixed up the problem and allowed CHECK to run through on all the files without needing to open/save individual files. But again, I don't know what implications these headers have.
I'm obviously not familiar with your code, but my guess is that upon a manual save from inside the program some kind of information or formatting change is saved into the .cha file about the Font by default, which is not happening when I edit in a text editor OR run things from the command box. This is probably not a problem that has been encountered before because I doubt very many people are importing the way that I am and batch editing to the extent I am (we have approximately 120 transcriptions to import from a project where transcription is already completed in lab-designed Excel worksheets). I should add that the .cha files I'm creating to start with are just a straight conversion of a .txt file. I did not use any of CLANs import functions. I wrote a VBA script to create a text file from the patched together information in our Excel sheets and I simply tell Excel to save it with a .cha extension.