Hmm. Thought: are you running Vista with EQ2 installed in the standard Program Files location? If so, Vista's built-in protection mechanisms may be blocking any attempt to modify files in the program directory. EQ2 stores the saved UI layout and settings in the program directory, and it can't save them if Vista refuses to allow writes there.
To get around this, you can disable Vista's file protections. You can also run EQ2 as an administrator. Or you can install EQ2 outside the Program Files tree, say in it's own directory under the drive root.
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