purchased N2200 a week ago, had trouble adapting to many non-robust features from its software and firmware, including unit restarts due to heavy BT/emule traffic. Among other problems, I think the download manager is of very low quality work.
Anyway, upon plugging in the 2nd drive on BAY2, the unit fails to identify it. Upon probing the Hard drive power connector, I do not see any 5 or 12V coming out of it. Tracing the cable back to the PCB, power is not coming out from the NXP power IC... I am questioning the quality of both hardware and software of this unit. Understanding this is an entry level unit, but it does deserve lot more attention.
I have the same feeling on the product after ~1 month of using it. There are features I was not able to use like CopyButton or BT download manager !!! Features considered as important criteria during my decision to buy this device ... and the support center is not giving me any hint on the troubles I have either after 3 weeks !!!
Comming back to your problem - I do not have an answer or a solution for you but I just wanted to confirm I am using 2 HDDs inside the unit in RAID1 and they are both working fine. Therefore I think the HW connection are ok. Are you using the same type of HDDs both in bay 1 and 2? (even this should not be the case, what else can we question? ) Did you tried the second HDD somewhere else and it worked ok?