as taco-man said, EQ2 updater should be closing itself before eq2 runs. Best way to check is to run the updater, let it boot into EQ2, and on the quicklaunch make sure the eq2updater window is closed.
If it is, press ctrl-alt-del and look in the task manager processes tab. If there is a process called EQ2_Updater.exe running then kill it off and try that, and then we can work out why it isn't closing. If it isn't there then the updater itself simply isn't the problem.
If the updater is closing fine then you might want to look at your UI and the setup of where the maps are being placed. You might have a corrupt file somewhere. Go into the EQ2map updater options and hit the re-download all files button. If that doesn't sort it, try running it without a custom UI installed.
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