Sounds like it could be a couple things.
Are you using a custom UI (like ProfitUI, Fetish, eXtremeUI, etc, for example) in addition to EQ2Map? If so, did you point the map updater to that UI's directory/folder? The map files will need to be in any custom UI folder that you may be using (which will be added to an EQ2Map subfolder within that folder), as that is the location your eq2.ini file is pointing to. If you did not point the updater to the custom UI, just cut/paste the EQ2MAP folder from your EQII/UI directory into the custom UI's folder.
If you're not using a custom UI, then you may not have the proper file in place (the eq2.ini file referred to above). Follow steps 5-7
here to set it up.