could it be that you have applied a filter?
AFAIK: MP3tag gets the files as they are presented by the OS. If the OS sees them then MP3tag should see them as well.
What does the status bar at the bottom show? Does the number of loaded files match the number of shown files?
There have been reports about left-out files which were damaged to such an extent that MP3tag would not load them.
So, if the files are new files, then please check them for integrity first (really with a tool, playing them is not enough).