So when you look at extended tags, you only see mp3gain-specific tags, and in that same extended tag view you don't see the tags you see in Windows Explorer?
If you can see something of what you want in Windows Explorer, it still strikes me as a form of corruption. In such cases, I usually try Foobar. Again with a duplicate copy to experiment, with just the standard Foobar config (just install and go with default settings), select a file, right click, and try utilities>fix VBR mp3 header, Rebuild Mp3 stream, and Verify integrity to see what you get in Mp3tag.
If that doesn't work I suggest you google for a free hex reader/editor, install it, and post some pics of what it shows on the right side of a file you view in the hex reader.
Some insight into what change in your system or how you used the files that may correlate to when you saw the change might help trigger more ideas, as well all the applications you used to play songs and what you use to process and tag your files that you think you used between the last time things looked OK in Mp3tag and when they didn't.