Sounds like you probably have multiple installs of EQ2 and that EQ2MAP is going to the wrong one.
Right click on the shortcut you use to launch EQ2 (the copy that works, the streaming version) and click properties. You'll see something under "Target" -- this will be the path to the copy of EQ2 that you're using to play the game, note that down somewhere. It'll look something like C:\SomeFolder\SomethingElse\ etc.
Now open the EQ2MAP updater and once it's finished doing it's updating, click on "Options". There will be a path listed under "Everquest 2" -- this should be very similar to what you saw before. If it's not, click the "Browse" button next to it and click through the folders until you get to the same end folder as you wrote down earlier. I recommend starting from 'My Computer' and if you can't find a folder that's listed in the path you'll have to turn on showing hidden folders.
If you need to show hidden folders, read this paragraph, otherwise skip to the next one. To show the hidden folders, open the control panel from the start menu and go to folder options. Under the "view" tab you'll see a line that says "Hidden files and folders," under that click the little circle that says "Show hidden files and folders" then click ok. Once you've done that you should be able to follow that path of folders until you get to the last folder listed.
Once you've gotten to that last folder (which will normally be named EverQuest II) click on the EverQuest2.exe file in the window once to select it then click Open. That'll get the installer updating the right copy of EQ2. Now, to get it to launch that copy you'll have to click the second Browse button and follow that path again. This time rather than selecting EverQuest2.exe you'll select whatever file it showed when you copied that path earlier, it'll be called something like LaunchPad.exe or Launcher.exe.
Once you've done that, click Ok in the EQ2MAP updater options window and it should start updating that new spot. Hope this helps.
One of these days I (or someone else) needs to make a nice step-by-step walkthrough for this with screenshots for XP and Vista/7, as we see folks with this issue quite a lot, since the updater looks in the older place generally rather than the spot for the newer installs.
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