Here are some of the MOS Notes which as further details about this issue.
How To Fix Missing Responsibilities For A User (Doc ID 429852.1 )
Missing Responsibilities after 12.1.3 Upgrade (Doc ID 1309852.1 )
Missing responsibilities in R12.1.3 (Doc ID 1423432.1 )
Missing Responsibilities of direct/indirect Responsibilities Assignment After Upgrade To 12.1.3 From 11i (Doc ID 1581955.1 )