This indeed is the primary symptom of AutoStart virus.
There is a cure, but you have to do things in the right order. Meanwhile, everyone, make
absolutely certain you have made the following setting:
In the control panel "Quicktime Settings", select "Auto Play" in the pulldown menu. Disable both "CD Autoplay" and "CD-ROM Autoplay".
This prevents the AutoStart worm (it is properly termed a worm) from propagating.
This is a serious worm with some serious consequences, especially for users of MacOS 8.1. You should determine if this is the cause ASAP.
You can find most instances of this worm by using Sherlock to search for invisible files. If there is an invisible application called "DB", you've got it. Or an extension called "Desktop Printr Spooler". Note the spelling; there is a benign extension with slightly different spelling.
If indeed you have this thing, the pauses are caused by the worm running its application to find new uninfected disks and infect them. It also will search out files whose names end in ".dat" or ".data" and overwrite them with nonsense. There are reports of this worm destroying the directories on the startup disk, although no-one knows how exactly. I had this happen, and one theory was that the AutoStart worm was the culprit. I'm not 100% sure, as there were also issues with HDT Version 2.0.5 and MacOS8.1 which also caused what Apple called "Total, catastrophic data loss".
Nice, eh?
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