Thank you for contacting Telerik Support.
You may have heard about we changed the way how the persistent classes are mapped in the database. Please make sure to visit my colleague Slavo's blog
about this change so you can get a better understanding on how the system works now and try to convert your module to be compatible with Sitefinity 4.1.
If that does not help you in some way can you share me more details about the custom module that is giving you hard time.
the Telerik team