MT is not inherently limited to 1500 mtu (under 2.9), but it does have such a limit on many types of interfaces.
Exceptions to that, that I know of, are:
(at least some) Atheros interfaces can be set as high as 1600.
(at least some) Intel pro-1000 interfaces can be set to 16110.
I don’t know of any 10/100 interfaces where MT allows large MTUs.
Also, the slightly larger MTU necessary for VLAN is allowed transparently on interfaces that support it. I.e. a virtual interface will work perfectly with a MTU of 1500, even if the parent also has an apparent 1500 MTU (if the interface allows it).
If all else fails and you are willing to, try to enable connection-tracking on all routeros (v2.9.x) units in the path and see if that helps. No need to worry about v2.8.x though Please let me know how it turns out.
Set mtu to 1500 before trying