Dustydw, After going over everything you have already done I would advise that you do a reset to defaults and then reflash the firmware one more time. If at that point if you still have these same issues then we are looking at a bad chassis.
I have a TL2000 that is out of warranty.  It has a single half-height LTO-4 SAS drive, on the bottom slot.  It complains that the left magazine is incompatible and gives an error of 9B 3B.  Basically it will try and try and try and try to scan (using the infrared emitter) the I/O slot, but it fails.  So when it finally gives up, it moves on to the second column and is able to scan the rest of the left magazine via the infrared emitter as well as via barcode.  And then when it finishes that, it scans the right magazine with super speed and no trouble.  I've tried all sorts of firmware versions.  Right now I'm on the newest firmware:  C.00 (A19). I have made sure that the prism/fiducial/clear-plastic-bit is totally clean and in the right spot.  I have made sure that the TL2000 chassis is completely level by way of a bubble level and a digital level.  There is no bending/twisting/etc in the chassis nor in the left magazine.  And there is absolutely nothing blocking the path.  The chassis is completely open right now, so if there was something in the way, I'd certainly know it.  And I have reseated every card, drive, board I can. I was able to get it to succeed in scanning even the first column of the left magazine a few times today, but I was unable to reproduce it after it succeeded once. Is there some sort of test I can do that will let me know what needs to be cleaned/replaced/adjusted/upgraded/downgraded/etc?  I did do the tests available via the OCD and the Web UI, but those all just come back with the "left magazine incompatible" error.  Nothing useful at all. Any tips, tricks, or ideas?  Any help is appreciated.  I'm at a loss.
TL2000 Error 9B 3B - Skips first column of left magazine