I'm suspecting there's a bit of metadata unrelated to ID3v2.3, not created by Basehead but by Cubase from which the files originate.
Just to clarify what I've done earlier: in mp3tag, I've removed the tags from all files. I then write these files without tag, just to troubleshoot and find out what's going on in Basehead.
In Basehead, when I open these files there and look at the Details panel. There's basic info like Filename, Bit Depth for all of them (I guess that's iXML that's still there? I'm a complete noob, don't know what I'm doing). Some of the files have a few fields that others don't. For the files that have these extra fields, the comment normally would show up as well (but now it's empty because I've emptied all files). Files that are missing these extra fields, also don't show the comment when I add it. Hope that makes sense. Would you be able to tell me what's going on there? Thanks again for the effort taken.