I've never heard anything about Junebug working with Aaron Cain, but I commissioned him to make me my shader and talked to him a bit. It was nice and easy. There are plenty of people making carved machines in that biomechanical style so I don't think you could say he's straight biting off of Cain, but Cain "borrowed" a lot from Guy Aitchison too, you know? I guess what I'm saying is there is nothing new under the sun, as long as you "borrow" with respect and try to evolve yourself, I don't see it being necessarily a bad thing. Junebug makes decent, pretty machines, and at least you can get them for under $600 :-).
With regards to the shaders sounding "wierd." The one I got from him sounds a bit different too. Similar to the Soba Pilot I had. Long frame geometry and long skinny springs. I just resprang it a month ago with some eikon bluesteel springs and it sounds "normal" now. Still runs nice and consistent. You could probably contact him about retuning them if your having a problem. He seemed nice enough on the phone.
Oh and make sure your clipcord or powersupply isn't going, I just spent an hour trying to figure out why my FK Galaxie was acting up till I realize my clipcord was crapping out on me haha.