I'd try to find the slowest bidirectional level shifter you can. The TXB's once they get into the higher supply voltages(1.8 and up) are trying to put out 0.6-1ns edges, and 10ns long high current pulses.
Not sure what your options are, but you can also try and make the programmer plug into the target board, or just shorten the cable as much as possible, or adding more grounds till it looks like it wants to work. Some series resistance on the signal line (just a bit, < 30 ohms) may also take some of the ringing and bouncing out of the transmission line without choking the one-shot so much it can't pull the bus up.
Even then, that's a specific one-off instance of it working, not for general use.