I'm not sure I understand the situation.
The TT video cards work okay in other slots, but not in #4 and #5? BTW, in your first posting you listed them as the last two slots near the bottom, but the 9600 is a 6 slot machine, so would the last two slots be #5 and #6? Or did you start numbering from #0? Just want to be sure we're discussing the same slots.
I think Apple actually labels them A1, B1, C1, D2, E2 and F2 from upper most to lowest. So do you have a pair of Twin Turbos in E2 and F2? And they do not work there? And if you move them to different slots they do work?
If the above is accurate, have you tested any other cards in those slots and what was the result?
The PCI slots depend on three chips, Bandit, the PCI Arbiter, and the PCI Clock Buffer. In my experience, I have found a couple of boards on which the PCI Arbiter was not well soldered. Touching up the solder joints restored functionality to the associated slots.
I can't remember the part number on the Arbiter at the moment. It's a little, square, PLCC chip with 4n pins, where n is an integer smaller than 8. So maybe a 28 pin or 24 pin chip. Might have been as small as 20. There will be two of them on the board, one for each PCI bus (the 9600 has two PCI busses).