stu: eliminate the obvious
The only way you can, er, the only way *I* can troubleshoot like this is to, one by one, eliminate one potential source after another. BUT, I always try to "eliminate the obvious" first. Another way of saying it is, "confirm the things I think I am already sure of" first. This approach always feels like an unnecessary extra boring step, at first, but I always force myself to do it (or, almost always) and I am always pleased when I did. Because I get a warm and fuzzy when I am actually, REALLY sure of something, only because I have gone throught the trouble of testing it out.
For instance-- you switched software, and got the same problem. So we can probably eliminate corrupt software as a culprit. You first thought it was something to do with the micing amps, but now you believe it is simply when any audio that you recorded yourself comes into the mix. I would confirm this knowledge with a few more dumb tests-- i.e. does audio that you didn't record yourself do this (recorded on another system, dowloaded, etc)? What if there is no 'mix' but just the one recorded track (i.e. try to make your tests as absolutely minimalistic as possible)-- is there still a pop? Answer these dumb ones: is it audio you recorded AND edited? Does the length of the audio matter?
Other questions (to rig dumb tests to figure out): Is it the soundcard? First of all WHAT soundcard are you using? Is it a standard setup?-- ie digi001 or Audiomedia for the Mac. If it is all standard it probably isn't a hardware compatability problem. But check out your hardware compatiblity lists/call the vendor (get stupid) anyway: i.e. maybe it's a version incompatability. Remember: don't make ANY assumption. Rig tests to confirm things you think you are sure of first. Prove dumb things first. Then you will have a level of confidence to move onto a less dumb thing. This especially helps if you are dumb like me.
Do the samething with the OS version vs the soundcard: make sure they're definitely deemed compatible by the vendors.
Maybe it's a connection problem. You can try switching cards if this is feasible, or minimally remove and reinsert the one you have (you would be surprised how often a bad connection fucks things up). You might be able to get a different card temporarily somehow. A lot of stores have return policies. I might get another brand. It could be a cheaper brand, just different. If another card works then you know you are on the trail, but not yet there. You can then try doing the same with another card of the same type as your original. If that works then you can figure it might be a defective card.
You might have a software compatablity issue or a configuration issue. To fix software related problems I always try to eliminate everything I am not testing. Make the whole thing as bare-bones as humanly possible. Turn off all start up software/device driver switches so that you are not running anything else, or at least as little else as necessary
Try to rig up real "stupid" tests, in general: i.e. one track, one little sound recording. Oh, and don't assume that if you can't SEE the spike in the waveform that it isn't there, but just not being displayed. Did you try cutting the spiked parts out and just playing the spiked/ unspiked original audio seperately what happens? Also- don't automatically eliminate the source of the problem being external to your computer/soundcard. Prove it! Any part of the chain is suspect until PROVEN otherwise with a test or two.
You can also be "creatively stupid" in your tests, but only after you have been just "basically stupid". Rig tests that mix variables, and see what happens. If you think you found the problem, or part of the problem, rig a test to confirm the theory.
If you approach the problem this way, move slowly methodically, and stupidly, like a big ole dumb bear, you WILL fix it. Trust me. Just remember: get stupid, and stop making assumptions-- even small ones. It may be annoying and frustrating, but this is the only way I know to fix computer problems myself and I have been doing this professionally (fixing computer problems) for twenty years.
luck,
-jk