Vanishing Footage after Capture

I log & captured MiniDV footage via my Canon ZR-85 onto a raided external "drive". I got the footage captured and it was all there in the project and in the Folder on the drive.
I saved the project and quit. Three of the four captured video files disappeared from the Capture Scratch folder. Vanished.
I relaunched Final Cut and, sure enough, three of the four clips were now offline. Spotlight confirmed the files were no longer to be found on my computer.
What happened? This has happened a few times in the past, so how do I stop this from happening in the future?
Just so everything is on the table: I am running Compressor at the same time, which is hogging the processor and sharing the raid. And two of the three vanishing clips had simple generic "file" logos (not the Quicktime logo I expected) before I quit Final Cut. However, all the clips played in the Timeline just fine before I quit.
Any ideas?
Thanks!
~Luke

Thanks for the response. My scratch disk was not set to the trash, though, so that wasn't it. Good idea though.
Near as I can tell, since I was running a bunch of system intensive processes at the same time, the computer just couldn't handle it. The footage is capturing just fine now that I'm not longer running Compressor in the background. Now why the footage then vanished after it had been on the drive is still a mystery to me.
~Luke

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