My guess is they weren’t wired correctly. They should sound like normal pickups in their respective modes. If you do try it again just buy the right switch. Which can give you 3 modes. For heavier styles you only need the series bucker and the P90. Ideal would be series, parallel, and P90. The single by itself I could live without although I occasionally use it on the neck.
So this P-Rails installation I did was 7 months ago, and yesterday I figured out that I wired it up wrong. I was getting a humbucker sound, but then when switching to either the Rail pickup I could hear the P90 was still alive, it's not supposed to be, it's supposed to be cancelled. So I did a quick check and found out I really messed up the wiring.
The P-Rails, with a Seymour Duncan "Triple Shot" can do the following,
Pure P90
Pure Rail
Humbucker in series
Humbucker in parallel
that's a lot of options, so many in fact I'm going to buy another one for the neck.
Are these pure P 90 tones, or pure Single coil ( rail ) tones? probably not, but, the Axe 3 is so powerfully flexible I'm confident I'll get close.
Maybe not the best player, and I don't like his distorted tone at the end but, this is a good video showing how to wire up the Triple Shot and other good tips and tricks.