strange behaviour after upgrading from Jessie to Stretch

[Gary Dale]

My "server" is a bit of an antique. It's a Gigabyte MA790GP-UD4H with a 
Phenom II 940 processor, an SSD and 4 2T drives in a RAID 6 array plus 
8G of DDR2 ram.

A while back I found it necessary to add a Vantec PCIe SATA 6Gbps card 
with 2 internal SATA ports after ports 4 & 5 on the motherboard stopped 
recognizing the drives attached to them. It's been running with that 
configuration for at least a year.

This morning I upgraded from Jessie to Stretch and things went haywire. 
I could successfully boot into the system using SystemRescueCD but the 2 
drives attached to the add-in card weren't recognized. My RAID 6 array 
was running degraded on the two drives attached to ports 2 & 3. Attempts 
to boot into Debian/Stretch were largely unsuccessful, with the computer 
usually locking up after reporting an error on an ATA device.

After a lot of fiddling I discovered that the HDs themselves were all OK 
but could only be accessed using SATA ports 0 - 3. However my 
boot/system  SSD and the BluRay writer both operate fine off of ports 4 
& 5. They also work when attached to the add-in card. I removed the 
add-in card and it now successfully boots into Debian/Stretch.

Both SystemRescueCD and Debian/Stretch are using 4.9 kernels but the 
former seemed able to boot while the latter wouldn't. I'm also confused 
by the problems I've been having with HDs not working when attached to 
some ports. Can any hardware gurus explain what's going on?