Yes.  the folders are created under the App_Code directory and the the corresponding entries are created in the web.config.

I had exactly the same issue trying to load the Survey module.

http://www.dotnetnuke.com/Community/Forums/tabid/795/mid/2108/threadid/124046/scope/posts/Default.aspx

In the end, I did a file-by-file comparison of the current Full Install package /Bin folder against all the files in my site's /Bin folder and I discovered several DNNSQL files as well as a BuildSupport dll file that I don't think should have been there.

I'm not totally certain, but I think it may be possible that I may have upgraded using a source version package at some point along the line. Anyways, removing those files seems to have the problem solved, so I really don't care at this point.

HTH
-eric