The initial firmware versions for the SAS 5/6 were pretty buggy ... could be all it was.  I don't understand what you said about swapping drives - there is no supported way to go from SAS to SATA (or vice versa), so the older firmware may have freaked out ... but it depends what you did to "swap" them. You updated the SAS 6 and the BIOS ... make sure you update the ESM firmware too.  Other system firmware should be updated as well (backplane, NIC, DRAC, etc.).
Have a SAS 6/IR card in a PE 2950 III.  Card is running FW 0.20.46.00 (or MPTBIOS-6.14.10.00).  Am planning to update the firmware.... Have a RAID1 volume defined, but it's not "activating" properly (shows as INACTIVE RAID VOLUME).  The two drives are just blinking green.  I know the disks are good because they were running fine prior to a reboot. In the card UI, I can "Activate" the array which seems to succeed, yet the array still shows inactive and the drives continue to blink. Any ideas?  Maybe I have a bad card?  Going to try swapping it out.... could I potentially use a PERC 6 card?  Have lots more of those around, but am unsure if it will honor the RAID config in place. Alternately, can I at least pull the data off these drives?  Presumably there's some sort of Dell-specific RAID information on the drive and beyond that is my data... I'm thinking if I put the drives in another system with an LSI SAS card (non-Dell) I might be able to get at it. Thanks.
Issue with SAS 6/iR on PE 2950 III