Hello, it's hard to say without seeing a sample of this happening. Are you using tabbed MDI or standard MDI. With tabbed MDI, it shouldn't matter since you only generally ever have the single selected document window's content in the visual tree at any given time. With standard MDI you have all the document windows' content in the visual tree. So if something related to your right-click menu examines the visual tree, then perhaps it's just due to there being a lot more visuals in the tree.
If you'd like us to take a look, please make a new simple sample project that shows the issue and email it to our support address. Reference this thread and rename the .zip file extension so it doesn't get spam blocked.