I have exactly the same issue. In fact searching the threads, there are numerous posts on this problem with no fix/suggestions.
http://forum.mikrotik.com/t/link-in-snmp-v3/53243/1
http://forum.mikrotik.com/t/link-rx-and-tx-via-snmp-values-dont-get-refreshed/34595/1
http://forum.mikrotik.com/t/cannot-see-the-link-info-when-using-snmpv3-profile-on-dude/38057/1
etc.
I have tried version 3.6 and v4.0beta3 and the issue is the same.
I have tried limiting the OIDs exported on the switches to just the “interfaces” MIB, but it makes no difference.
If I use SNMP v2c it works fine. There really is a bug with SNMP v3 that needs investigating.