If I had your issue, I would install the remote debugging tools on the IIS server to be able to attach my debugger to the distant process on the server.
This would allow analyzing and tracking down the problem.
There is an excellent article on CP about remote IIS debugging; there:
Remote IIS Debugging : Debug your ASP.NET Application which is hosted on "Remote IIS Server"[
^]
Not exactly a solution, but maybe something on the way to the resolution. Anyway, hope this helps.