Seems like you have encountered a bug. Post a message to support@mikrotik.com
Are routerboard software the same for the boxes?
This could be solved by using any led on the switch.
Fixed light eth1
Blink light eth2
I did try to use a script to show signal strength for one link by flassing the quality.
See here:
http://forum.mikrotik.com/t/using-wifi-or-user-led-to-show-signal-strength/125496/1