Cool, glad it worked. The reason for the problem and why that fixed it is that Mono implemented batch JIT compilation recently, and even though the WebPart stuff is left out of the dlls in the /bin folder, Mono was finding those .aspx, and .ascx files and trying to JIT compile them and since one or more of them have references to WebParts the JIT compilation was failing. Before they implemented the batch compilation it never JIT compiled anything until a request came in for the file, but now it crawls around and finds all the files and tries to JIT compile them all in a batch on the first request. So we have to get rid of these files. The Mono team has a solution for this as mentioned here, so I can resolve this also with web.config settings. Actually I did resolve it before but looking at the documentation they changed it since my initial look at it so my fix needs to be updated for their new implementation, thats why its not working. The new fix is much easier anyway. By marking some ignore paths we won't have to worry about deleting those files.
Best,
Joe