As I can't see the things Chops can but doubt that changing the layout would have this affect I'll ask a simple but probably obvious question that you might have looked at already.
Did you verify that the link for the DKP Menu on your site is correct? Is it possible that the problem is that the template doesn't have the correct link?
Another test might be to go to the advanced layout and download the last copy of your site before you dropped in the template and re-upload it. If your DKP is correct after that then the issue has to be a link name.
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Six Demon BagJack Burton: Hey, what more can a guy ask for?
Egg Shen: Oh, a six-demon bag!
Jack Burton: Terrific, a six-demon bag. Sensational. What's in it, Egg?
Egg Shen: Wind, fire, all that kind of thing!