This sh*t is way over me.
however i am happy to replicate problems and do some more diagnostics to figure it out -
The only thing I can think of ( other then contacting the vendors ) is setting up four simultaneous packet captures, one on each server machine, one on each side of the switch. Then compare for discrepancies.
A Lot of trouble for something that is now working!

Just a couple of links I came across that may or may not help:

Check System Requirements for Intel® I/O Acceleration Technology (Intel® I/OAT)
Jumbo Frame Clean Networking Gear


also, if this actually applies ( from download html files, self-extracting, User Guide for Intel® Network Adapters )
All equipment on the network must also support the larger frame size. When setting up Jumbo Frames on other network devices, be aware that different network devices calculate Jumbo Frame size differently. Some devices include the header information in the frame size while others do not. Intel adapters do not include header information in the frame size. When configuring Jumbo Frames on a switch, set the frame size four bytes higher for CRC, plus four bytes if you are using VLANs or QoS packet tagging.