Hi,
I'm not sure if this is the correct section of forums I don't see how the problem could be related to MPLS itself.
It looks like during replication some buffers are exchausted. You are right that avoiding fragmentation could be one of the possibilities to aleviate.. if it's THE problem at all.
AFAIR FCIP will use TCP for transport and not raw IP? If so you can adjust MSS (ip tcp adjust-mss) on an L3 interface of Cisco routers.
MSS is typically MTU - 40.
Marcin