How do I prevent my Mac Pro from  hanging up in a start/stop loop?

My Mac Pro has a strange behavior I need help with. This computer is used almost exclusively for audio recording in my studio. I run Cubase 4 as my primary sequencing software. Everything will be going fine during a session, and then the software will abruptly hang up in a *start/stop loop*, stuttering back and forth between these two functions for up to 2 minutes before stopping. During this loop problem, the start/stop transport buttons alternately light up and the song starts and stops. Nothing I have tried will interrupt the problem. It just runs its course and then stops, usually between 30 - 90 seconds.
Interestingly, the same behavior shows up in other applications and in the Finder. In Quicktime and iTunes, it shows up as a start/stop loop. In the finder, it will shuttle back and forth between two related functions and beep each time. In word, it will show up as a key stick, typing the same letter over and over.
Needless to say, this is all very frustrating and embarrassing when clients are here. Any help will be greatly appreciates. Let me know if you have any additional questions.

I'd begin with repairing your drives with Disk Utility and Disk Warrior; clone your system to another drive, and check for corrupt files and prefs.

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