Is there any way to tell the card to forget about not having a BBU and behave as if it did?
Short of modifying the code...I do not know of any.
Well, I've now got BBUs on order for the three identical machines to see if that does anything to improve matters - I'll report back when I've fitted them. A glance through the 2.26.05.007 driver code shows no references to the BBU, so the different code paths (with BBU and without) must be in the firmware itself.
If your card is on a PCI riser try running it plugged directly in the slot (if you can) and see if that helps.
He said his card is directly plugged in.