they said in an interview (the wire's invisible jukebox yonks ago) that they got into computers with chiastic slide. before that they had been mostly using hardware, albeit in an original way. but i can really hear software at work on chiastic slide, lp 5, ciclli suite and ep7. i also read once sean saying he went to math class (this was around '96 or so), so I'm guessing it was to help with programming. so i reckon between max/msp, reaktor and fm7 and their nords, this is where their sounds came from.
but its cool that they've sort of turned their back on software since releasing untilted, totally hardware-driven live shows. Ae can make Ae-music using whatever they turn their hands to.