Well, first of all, you have to unquote them;
Code:
<!-- <maps>C:\EQEMU\Maps</maps> -->
to
Code:
<maps>C:\EQEMU\Maps</maps>
It's quoted so you can see what EqEmu defaults too, and if you want to change.
This probably will not solve your problem , and you should set it back (don't confuse yourself anymore).
What might be happening is, your Perl is not being found by EqEmu