Kevin,
MSS is the value of the data that a packet can really transport, the MTU is the gross value of the packet, the IP header of 20 bytes and the PCP header of 20 bytes are just the values when you don't have any reason to change the MSS value. The Default MSS with the above mentioned values is 1360, however as soon as a VPN or any other encapsulation method is used in the communications line it will need to start fragmenting as that IPSEC or GRE header will be added into the packet, a GRE packet is 24 bytes, which will end up in leaving yopu 1400 -20-20-24 = 1336 bytes, which is the actual possible MSS in case of GRE.
What happens when you try to put 1360 bytes inside a GRE packet is that the packet will be fragmented.
The best document about this that i have ever seen can be found here, it also explains PMTUD (Path MTU Discovery)
So the MSS value should be tested and normally you should be able to do a end to end test, there is a small program called TCP-optimizer, which runs on windows and will tell you the right MTU value for that connection, just substract 40 from it to get the MSS.
The MSS value should be set via GuiDBedit, on the interface of the gateway object you will find a MSS value, default=0
Regards, Maarten