IanP, Would biasing resistors help on the transmitter rather than the receiver? I've seen examples of biasing those lines on both the transmitter and the receiver. The peripheral receives just fine, but the receiver on the other board can't be changed at this point.
kmr, I will take a look at those signal levels. I have looked at them briefly, but not since I got it working on the shorter cable (before I tried longer lengths). I'm using the MC3487 chip as my transmitter and MC3486 as my receiver with optional 100 ohm parallel termination through a jumper. Switching the termination on and off doesn't make much difference. I'll look into an amplifier. I was under the impression that the 3487 would be sufficient, but good point, maybe that's where the issue is.
Added after 4 hours 19 minutes:
Well, thanks for everyone's help, but actually I figured out the problem. Just had a break in the power line to the 3487. Weird thing is that it still worked without power on the 3 foot cable. Oh well, figured it out.