My Everquest 2 directory is on my D:\ drive and I had no trouble installing the eq2map updater. I'm not sure why it wouldnt install correctly for you. The eq2map program will install it self on the C:\ under program files and yes thats intended. If you already have an eq2.ini it will read that ini and install it in your current custom UI folder. If you dont have a eq2.ini then it makes one for you. So if you already had a eq2.ini then it wont modifiy it.
The problem shown in the picture you attached is a known issue and is mentioned here that its being worked on:
http://www.eq2interface.com/download...fo.php?id=3509 (scroll down to Known Issues twords the bottom).