Make sure that your setup fits in MTU limits of your hardware, see
http://wiki.mikrotik.com/wiki/Maximum_T ... uterBoards
Default mpls-mtu is 1508, also for VLAN interface. If packet gets labelled with 1 MPLS label and 1 VLAN tag, your hardware (routers and switches) must be able to transmit 14 + 4 + 4 + 1500 = 1522 byte packets (not counting FCS). Other than that, there should be no difference in running MPLS over VLAN interfaces.