Intel Mac :: Crackling When Recording Or Playing Audio

I'm having a very annoying problem, and I simply can't figure it out. Recently I updated my OS from Leopard to Snow Leopard, because I had some problems with the firewire connection to my fireface 400 sound card. So far this seems to have solved the problem, and for a couple of weeks I was actually able to get some work done. Now a new problem has occured: 

When I input audio (i.e. trying to record something) I get some really weird crackling noises. It's very different how loud they are. Mostly they are at the same volume as the instrument I'm recording, and normally it sounds very digital. I've tried hooking a presonus firebox up to my mac, which gave me the exact same problems, so it can't be the fireface that's the problem. The problem is not something that occurs, when recording, but simply when sending audio into the mac. There are absolutely no problems when playing back files from iTunes and Logic.  

I've tried repairing disk permissions, and ran all the  tests in techtool pro, which all turned out fine, so I'm having a hard time believing that it's a hardware issue even though I've had problems with the firewire connection earlier.  
Though it does not sound like clipping, the problem seems to  occur more rarely, when playing soft, which just makes it even more weird. 

Model Name:iMac  Model Identifier:iMac9,1  Processor Name:Intel Core 2 Duo  Processor Speed:2,66 GHz  Number Of Processors:1  Total Number Of Cores:2  L2 Cache:6 MB  Memory:4 GB  Bus Speed:1,07 GHz  Boot ROM Version:IM91.008D.B08  SMC Version (system):1.45f0 

Everything is up to date, it just seems like something has been messed up somewhere inside the mac. Next step is to wipe the hard disc, but I'd rather not do that.

Info:
iMac, Mac OS X (10.6.8)