I used to put the resistors in the cable itself. Xilinx CPLD was supposed to be 5V tolerant, but it was discovered the hard way that it wasn't after all.
what resistor values do you use?
My Atari with the UItimate 1MB and with VBXE (both from Candle) is dead since a few months and I recently decided to take a new motherboard and upgrade it with the extensions taken away from the dead Atari.
Luckily everything seems to work well, besides the issue, that I already experienced with the old machine (when it was still working).
The following carts do not work properly: The!Cart and MyIDE II (all others do). Back in time Jürgen (tfhh) was looking at the cart signals of my Atari with an oscilloscope and pointed out that some of them were not stable, meaning that my Ultimate 1MB was not be working perfectly...
Maybe it is related to those resistors? I simply took them over (didn't even measured them). If I remember well, they were originally provided by Candle.