[myrandomcomment]

The paths on the network with the MLAG is NOT likely the issue. There is a serialization delay different between the NICs in the NTP servers and switches. 100M takes more time then 1G which takes more time then 10G which takes more time then 40G. Also the UI kit is store and forward (not sure on the 10G but the desktop one is) switching and the Arista kit is cut thought (at around ~500 byte packets IIRC). The end to end paths are not the same given the link speed difference and that is the source of the variations. The MLAG hashing is in hardware and will not have an effect, also IIRC you can set the LAG hash to be SRC/DST on both L2 and L3 even on a L2 link.