MSS is not configurable on the system outside of PPPoE which you probably aren't dealing with, you can see the negotiated MSS with a packet capture and looking at the TCP SYN packet during the TCP handshake for a session.
The only scenario I can think of where MSS would be impacting you like this would be if the MSS is negotiated to a value that the GRE tunnel back to the controller (assuming tunneled) can't support, that would point back to MTU issues in the network that could be adjusted. Could also just as easily be jitter, channel busy, and solar flares.