Make sure fans are connected to the right connector... For SC5650DP, fans should be connected to Chassis Fan 1, 3 and 5, and of course the CPU fan.
As for RAID in Linux, isn't is easier to use the onboard Intel® Embedded Server RAID Technology II? See Demo: Configuring Intel® Embedded Server RAID Technology II and Demo: Loading Intel® Embedded Server RAID driver during OS installation.
A chasis fan was indeed pluged in the wrong connector. But I still not understand why I didn't have the fan problem before the BIOS update.
For the RAID, I don't know much about Intel's RAID technology. As I don't use either RHEL nor SUSE but gentoo I don't know if it would be easyer. But it is still more a workaround because I think the AHCI ROM should'nt hang when pluging drives with Linux RAID autodetect partitions.
Thanks for solving my fans issue
They are on the compatibility list, both are WD5003ABYX from Western Digital. I forgot to tell, but thought it was obvious. Before creating partitions on them and rebooting, they were detected by the AHCI ROM without any problem, and i was even able to hotplug them.
Seems that there is a problem with the AHCI ROM and the Linux RAID autodetect (0xfd) partitions…