I have seen this a lot with my other extensions. Try this - Go in to your SEF URL list and find the URL that is having module mapping issues. You'll probably (maybe) will find two duplicate SEF URL's pointing to two different real URL's. This is a problem
You can unpublish the one you don't need ( I recommend a lock and block to so it does not regenerate after purges)
You can rename one of the menu links or whatever SEF is using to generate the links.
I have the same issues in categorys and sections. Where a real url is generated for both the default and the blog layouts. Thought I'd save you the hours it took me to figure this out. Hidden menu's with duplicate menu names is the first place to start- or was for me atleast. You'll have all these or different issues with any SEF tool. Its just a matter of getting it tuned and set up.