🚀 go-pugleaf

I have a problem with the directory structure on my IBM's 20 Meg hard 
disk.  In a subdirectory (\tp5\source), I find a copy of the root directory
that acts just like a subdirectory i.e. when i delete files in the directory
\tp5\source\games, the same file is deleted from \games.  Because of this,
programs like XTree, when looking for all of the files on disk will find
\tp5\source and then \tp5\source\tp5\source\tp5\source\tp5\source (you get
the idea), and then crash, proclaiming "too many files."
I've tried to correct this, but like I say, trying to remove one of the
"extra" directories removes it from the root directory.  It appears that
I will either have to 1) learn to live with it (the circularly linked files
dont take up any extra space), or 2) learn to remove a non-empty directory
(\tp5\source) without removing the root directory.
One idea I have is that possibly DOS4.0 is causing this problem.  Although
I upgraded to 4.0 from 3.3 several months back, the problem has only recently
surfaced.  Doesn't 4.0 use larger FAT's that could collide with 3.0's?  Perhaps
I need to back up the drive and reformat with 4.0.  Anyone think this would
work?
I suppose I could hide the \tp5\source directory but that would not really
be stopping the problem in my opinion.
Has anyone ever seen this before or have any good advice?

BTW, I have RFTM and several other books, to no avail.  Please dont tell me
to do so again.