I'm not entirely clear on what you mean by "clipping" which usually refers to a waveform that often peaks 'above' 0dB and therefore sounds distorted and crunchy. From your description, it sounds like the issue is more likely dropouts where the audio is coming in faster than it can be written to disk (for various reasons) and therefore is missing small snippets here and there.
In either case, I would always recommend closing any unnecessary applications when recording - especially audio applications such as iTunes. If the audio is indeed "clipping," then that implies the incoming signal is too loud and this would need to be adjusted either in the OS X Audio/MIDI Setup, your mixer device feeding the signal to your audio card, or the original audio source. If it is, rather, dropping out and missing small bits of audio, there are a few common methods to prevent this: first, increase the size of your I/O Buffer under Preferences > Audio Hardware. Unless your recording while monitoring existing tracks, I would recommend bumping this up to 1024, or in incremental steps from your current setting until you no longer experience the problem. If this makes no difference, ensure that no applications that might otherwise be heavily accessing your hard drive are running while you record. This might include download managers or torrent clients, drive cleaners or archiving utilities. Even antivirus software can take a heavy toll on performance while writing data to disk.
I'll add that since the public beta was released, significant improvements have been made to the performance while recording in multitrack and I'd suspect many of these issues will be minimized or no longer an issue. I would recommend verifying with the 30-day trial edition when Audition is released.
