There is only one warning:

"my" variable $section masks earlier declaration in same scope at perl
+man.pl line 179.
Scouting man directories
Starting UI ...Use of uninitialized value $id in hash element at /usr/
+lib/perl5/vendor_perl/5.10/i686-cygwin/Tk/After.pm line 39.
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etc.

Removing the second my declaration does not change the result (nor should it, looking at the code).

I am puzzled as to how the debugger "fixes" the code. The implication from error messages is that an undefined value is being used where it is not permitted; how can the debugger fix that? In fact, it shouldn't. The reason I even tried the script in the debugger was to see where the problem was and to try to fix it.