Afte Upgrade from 11.5.10.2 to 12.1.3, the Custom Application is restricting processing and reportin

After upgrading to 12.1.3, is anybody else experiencing issues with responsibilities assigned to a Custom Application?  We have a number of Data Entry and Data Inquiry responsibilties that cross modules (e.g. AP and AR).  A standard practice was to assign them to a Custom Application - however, this functionality didn't really seem to upgrade well. 

Anybody have any suggestions?  We're finding processes like Create Accounting and the Account Analysis report don't work with the Custom Application...having to maintain more responsibilities now, which is a step backward - not forward.

Any suggestions would be greatly appreciated!