Are you just using file/send to/compressor? Wonder if trashing your plist for compressor might fix this and/or trashing prefs for FCP... It's not a bug nor is it a bad setting you could change don't think.
If you export a self contained movie and open that in Compressor instead, then I'll wager it will work OK, and still allow you to work in FCP during the compression... If you export a non self contained file, it should work OK too and be pretty fast if all of the renders are complete in your source sequence.
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