Zig, I had the same problem as you and it was driving me insane.
Go in and uninstall the patch through the control panel. When that's done. Look in your program files, and I'll bet you have an eqemu folder out there. Delete that one. Now go back into the EQ folders and run the patch setup, it will start again and this time give you the option to put the file into the EQ folder (use browse). Now you should have the patch again on the desktop. Make sure you check the box "Run EQ" that should work for you. Let me know.
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