... your $PathOnly is in double quotes, so the backslashes there are interpreted as escape sequences.

##</code><code>##

c:\@Work\Perl\monks>perl -wMstrict -le
"my $PathOnly = qq{c:\Dir1\Dir2\taint_so};
 print qq{>$PathOnly<};
"
Unrecognized escape \D passed through at -e line 1.
Unrecognized escape \D passed through at -e line 1.
>c:Dir1Dir2     aint_so<