So I was testing a JP BFR, and I noticed a minor difference in tone (magnetic pickups) when I swap the cable between the top and bottom jacks... is that a normal thing? Can anyone confirm this?
The difference is likely the output buffer on the dual output. It negates the effect of cable capacitance, so it might seem brighter. If you used a low-capacitance cable you probably wouldn't notice the difference.
It seems to be that... however, I don't remember noticing anything like that on a standard JP6 (first model, with original custom DiMarzio pups). This behavior also exists on the old models, or that's something new?
Also, could you elaborate a little further on this "output buffer" thing?
A 'buffer' is an always-on amplifier used to isolate the signal from effects further down the signal chain. It's necessary to provide the right kind of output for the piezo signal, and to mix the output from the magnetic pickups with the piezo. (Whereas you don't actually need it for the magnetic pickups on their own).
The nature of passive guitar circuits is that they're affected by the capacitance of long cables. The longer the cable you use (the more capacitance), the more high-end is lost in your signal. However, when you buffer the signal (through the onboard preamp on your guitar), the cable doesn't have any real effect ... so you keep more high end from your guitar.
The older model JPs had a separate, passive output for the magnetic pickups and an active output for the combined output. So that's where you'd noticed the buffer/cable effects.
On many of the newer MM instruments, all the outputs are buffered (the preamp is also used to provide the boost functionality). So you may notice this depending on which model you've got.