What format are you bringing your audio files into Captivate?
The generally recommended format is: WAV 16-bit PCM
If that's not what you're currently using, try adjusting your audio editor to output those specifications.
I'm not using any audio editor, I'm recording in PowerPoint.
One way to deal with PowerPoint is to treat it as you would any other application. Present the PowerPoint in its own window and record that using Captivate. Then you could add the audio narration using Captivate.
I'm with Rick on this one. I would never willingly choose to record audio in PowerPoint if Captivate is available to do it. Captivate has much better recording options. Of course Adobe Audition is even better, but Captivate does a very good job.