Ah, I see the problem.
I assume you are using the right click menu to dismiss the pet ? If so there is the problem. Most unit frame addons aren't allowed to use the right click menu to do things such as inspect people or dismiss pets or set focus etc.
However there is another way of doing this. Hunters have an ability called dismiss pet. Simply put that on one of your bars somewhere and use that when you want to dismiss. perhaps next to your call pet button perhaps.
Here's a screenshot to show you what I mean. And as you can see I have carbonite and nUI running at the same time.
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