At 40 mt it shouldn’t make much of a difference, but at 300 m alignment is important.
Just in case a detailed way to align (related to the nRay, but aligning two Cubes should not be much different):
http://forum.mikrotik.com/t/problems-aiming-nray/174150/1
This said 1.2 Mbps seems way too low, check anyway the RSSI, and Tx sector info and the on the status of the 60 GHz interface, see here for an example:
http://forum.mikrotik.com/t/cube-alignment-acceptable/169784/1
Then, post your configurations, follow this:
http://forum.mikrotik.com/t/forum-rules/173010/1
But the pairs come largely pre-configured, you can also compare your configuration with the one(s) posted recently here:
http://forum.mikrotik.com/t/wireless-wire-cube-preconfigured-plug-n-play-doesnt/173973/1
In that same thread Amm0 evidenced a possible issue with RSTP when the Cubes are connected to enterprise level switches:
http://forum.mikrotik.com/t/wireless-wire-cube-preconfigured-plug-n-play-doesnt/173973/1
but cannot say if it would slow the connection (I think it should prevent it or make it unstable) 
Judging from people having issues with them that posted on the forum it is however strange, the reported issues I have seen are mostly with difficulties in connecting to them, not about (so much) slow links, is the behaviour the same if you do the test instead of through the CISCO devices between two PC’s (or between a PC and the Cisco device on the other side of the wireless link)?