RX over is good jumbo frames over the 1518 byte size. I wouldn't expect this to be a problem with upgrading the stack. Can you provide a little more detail on where in the upgrade process you are failing?
When packets need to traverse between stack nodes some packets could certainly be greater than the 1518 byte size as when they need to go through hi-gig links, a hi-gig header of 12 bytes would be added.
My recommendation, if the upgrade is adding the image to the master node and not the other nodes, would be to download/install to master and sychronize the remaining nodes to see if that works.