I had the same problem, probably since I installed VStudio 2005 beta 2 (including .net framework 2.0)
After a few tests, I did manage to make EQ2MAP work again, modifying your xml file to this :
<?xml version="1.0"?>
<configuration>
<startup>
<supportedRuntime version="v2.0.50215"/>
<requiredRuntime version="v2.0.50215" safemode="true"/>
</startup>
<runtime>
<assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1" appliesTo="v1.0.3705">
</assemblyBinding>
</runtime>
</configuration>
copy/paste this in a file named EQ2MAP_Updater.exe.config and maybe it will also work for you