Why don't you unplug the Superchip and connect the amal valve back up and see what happens? You may find it actually gets better (you may need to adjust the actuator). Mine had a powerchip in it when I bought it and it just didn't run right. When I took it out it got loads quicker. It might on yours too because on paper you're running less power than standard.

My amal valve clicks like crazy when it idles with the superchip plugged in. I also get the annoying ECU ROM failure code logged as Stu says. However it does seem to run quite well apart from that.

Stu - if you're reading this - how much power can one of your chips get out of the T25 with the standard turbo? GGR claim to be able to get 305, but from what I've heard these are nearer to 280 bhp. Hardly seems worth replacing a 260ish superchip with one of those :-( but I'd love some more power.