Is the path from the server to the router the same as the path from the router to the server?
There is a long standing issue with SNMP on RouterOS not replying from the IP to which the request was addressed when the reply packet leaves the router via a different interface with a different IP address.
http://forum.mikrotik.com/t/snmp-doesnt-work-with-asymmetric-routes/58545/1
In 6.40 and later, we now have the ability to specify the src-address for SNMP traffic. That should help with this issue.