Make sure your ram is OK. I had weird intermittant glitches in my Protools system when bouncing files and it turned out I had bought the incorrect ram for my Mac, OOPS. Works great since.

free up as much ram as you can. If its not a dedicated audio computer disconnect the network cable, and go to Start : Run and type "msconfig" Click the startup tab and deselect everything except the software for your soundcard. If you can't figure out what that is, go in and deselect everything that looks like adware, virus software or any of that. It'll make you restart your computer and then see if your sound card still works. If it does you might be alright. Increase your latency and make sure you have the most current driver for your soundcard.

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Its all about Memory

The best thing i can suggest is that you expand your memory. RAM is key in cool edit pro 2 since thats what i have been using for a good while now. if you get any type of glitches like loud popping noises. save and restart your app. also you can solo/mute certain tracks for the better of the recording and then mix down later. but like i said b4 the more memory you have the less fucc ups you have to worry about with cool edit pro....or you can switch to Sonar 3 producer edition which you can find on any p2p file sharing program.
Good Lucc!