Hi,
Agreed with Thomas answer. Yes, console are behaving independently and that's a complex thing to deal with. Basically, if you use MCS, then you have to use *ONLY* MCS for profile definition/modification/deletion/deployment. If you do something on an MCS profile through the IM, then, data are not synchronized anymore and that's wrong.
I would say there's two way to go now:
* MCS only
* IM/AdminConsole
However, as long as you use MCS for profile and IM/AdminConsole for small modification, probe deployment, data consultation, robot management and all thos administrative actions, you should be perfectly fine. The gold rule here is: don't modify anything pushed by MCS outside of MCS.