Hi,
I just solved it after few days with no success.
It was just as simple as registering assembly.
We have a clustered environment and failure was only on one node.
See resolution here:
https://social.msdn.microsoft.com/Forums/aspnet/en-US/754f2a9f-4fbb-4805-af19-cff1d49fba94/systemiofilenotfoundexception-when-use-map?forum=biztalkgeneral