Like jnils said to the OP, you probably have 2 installs of EQ2 without knowing it.
Open the patcher, click the tool button (gear and tools icon) and click open game directory. That will show you which directory your launcher is using. Make sure that matches the one the EQ2MAP updater is pointed to. If it is set up correctly, you should have an eq2map folder in your UI folder in that EQ2 install.
If you have that folder in there but still aren't seeing maps, check your eq2.ini and eq2_recent.ini and make sure they have EQ2MAP listed as the UI name instead of Default.
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