I just recently stumbled upon the same problem, only to realize that it's almost 2 years since you encountered the problem.
Did you gain any insight on the case since then?
Tried with IOSXE version 3.6.3 and upgraded to 3.7.3 hoping the issue has been resolved, no luck so far.
No matter if I set the flow control settings to on/off/desirable, the flow control operational indicator stays "off" with no pause frames received (client is a multimedia terminal that, so I am told, sends the pause frames)
Currently I am thinking of opening a TAC since this looks exactly like the BugID CSCul33405, which should be ressolved in newer software versions.
#show flowcontrol int gi1/0/25
Port Send FlowControl Receive FlowControl RxPause TxPause