I have an RES2SV240 connected to an Adaptec 6805 (I also connected it to an LSI controller as well and the same behavior takes place). When I connect one enclosure (that has 2 ports) to the furthest rightmost ports on the card, it sees all drives in the single enclosure. When I add 2 connections to the next most rightmost connections (4 rightmost taken up at this point) to the other enclosure, it only shows 3 drives.
I've ruled out it being the other enclosure by trying each one individually. I've also swapped out the 8087 cables to ensure it's not that either.
I seem to recall there being a guide that actually showed cabling order, although I thought it was only relevant if you had 2 inbound connections, not a single one but I can't seem to find that.
I don't know how the RES2SV240 will work with the Adaptec* RAID controller, but we have tested it with Intel and some LSI RAID controllers. You can see what has been tested in the http://www.intel.com/support/motherboards/server/sb/CS-031815.htm Tested Hardware & Operating Systems List for the RES2SV240.
The RES2SV240 is configurable allowing for either 4 or 8 incoming ports and 20 or 16 outgoing ports. You can find details in the RES2SV240 http://www.intel.com/support/motherboards/server/sb/CS-031813.htm Hardware User's Guide.