Well guys, I tinkered around more tonight. Here are my findings:
-The pops, while not showing in the waveform, are there somehow. Even when I take the raw wave and convert it into some other format with another program, the pops and clicks are still there.
-I used 4 different hard drives, with three different methods of connection, all garnered pops.
-I unplugged everything and turned off everything that wasn't Axe II or Reaper(or Audacity or GarbageBand, all tried individually) still have pops.
-I used both system output and Axe output, still get pops
-I plugged in POD X3(also via USB) and got no pops? Plugged Axe outs into POD(essentially using POD as interface...yuck) and while it sounded....well...odd...there were no pops. Line6 A/D conversion is....well...I don't need to go into that.
-All through out all of this, I monitored Reaper's performance. The disk write speed never exceeded 149B/s and CPU usage never went more than 5.9%(with the exception of right when I start recording I would get a 20%ish spike but there were no pops here)
-Sometimes, there is only a few pops, other times the take is unusable. No rhyme or reason that I could find point to either case.
-When I select to output via the built-in system, there is a latency there. It's not terrible but I can deff feel it and when I tried to play along with something, my timing was all crap.
The last bullet item I think is the heart of this thing, somewhere there is a latency or buffer issue. It isn't Reaper specific so I don't know if there is a setting in Reaper that can compensate for it. It seems to be something in the OSX system vs something in the II. Maybe the driver? I'm no 'puter tech. I'm going to compile a little more stuff before I send a note off to Cliff(if you are reading this, I'll send you and email soon, I don't want to waste your time so I'm trying to get as much detail as possible and will include clips) and probably won't get to that until the weekend.
For now, I'm jamming the heck out of my II but for recording I'm kind of dead in the water. I also going to try another computer as soon as I get access to one.
Ohh and did I mention that the HBE model makes my pictures on the wall shake....honestly I didn't mean to turn it up that loud...honest...