Well this may be your problem - you need have a single "default" directory called "C:\EQEMU" inside C:\EQEMU, you need to have quests, maps, pluggins, etc. but the executables should reside in "C:\EQEMU" (I'm trying to make this as simple as possible for you, so it works and we avoid confusion).
You can always copy the old binaries back if you are un-happy with the new ones. Or better yet, you can make a new directory in C:\EQEMU and call it "backups" (C:\EQEMU\BACKUPS). copy everything in there before you add updates, so you have a working backup.
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