No, all the PCI-E slots seem to be working now. Not sure why it started working, but they are working. My problem was that sas2flsh in FreeDOS doesn't work with the X9 systems. I wish I had known that and avoided this entire path...possible that ur card has damaged the slot, I do remember some cards were proprietary to certain boards and required taping, was a long time ago i had read a thread similar, and the board slot was damaged.
I've now ripped out the X9SCM-F + E3-1220L combo. Just too much hassle for building a bulk firmware flashing machine. I have a partially defective X8DT6-F sitting on the shelf and decided to use that. I disabled the onboard SAS controller with jumper setting (to avoid conflict with PCI-E HBA cards that I want to flash) and only have a single cpu in it (E5620). Just ordered a L5630 for $6 so that should reduce another 30W or so. It currently idles around 100W, so that should bring it down to 70W or so. Not as good as the 35-40W of the X9SCM-F+E3-1220L combo, but the following benefits outweigh the power savings:
1. all the PCI-E slots work, regardless of # of CPUs or how many PCI-E lanes the CPU can provide. I can now flash 5 cards at once, which is even better than the X9SCM-F. so, uncomplicated, working PCI-E slots and more of them.
2. DOS programs like sas2flsh.exe actually run without issues and I don't have to resort to UEFI shell. this is a convenience for me since I already have batch file programs that do the firmware flashing in bulk; I would have to figure out how to write UEFI scripts if I had to use the UEFI shell.
So, for anyone who finds this thread and are looking to build a machine for bulk firmware flashing, I'd say go for a X8 platform. The number of available PCI-E slots is a critical factor here, and having that tied to CPU features just complicates the issue too much. It's definitely not as power efficient, but the overhead of running the machine is more than compensated by the abundant number of working PCI-E slots with a single CPU.