are you exporting selfcontained quicktimes with current settings from fcp and then bringing them into compressor? Are you using qmaster to set up a render cluster?
It's possible you're seeing an incipient drive failure.
Also, make sure you have at least 10% free space on every drive and closer to 20% on your boot drive.
Drive read/write speeds decrease enormously when they're almost full.
Also, run diskwarrior (if you've got it and buy it if you don't) on all drives and run disk repair from the disk utility.
Thanks for your response, Micheal. In looking around for a solution I did see several posters suggesting exporting a .mov first, then importing that into Compressor. I have always gone from the FCP timeline, and always been able to get away with letting it encode overnight to find successful completion the next morning. Yesterday I learned that there are clear advantages to exporting QT first so will start doing that.
I need to find a simple fools guide to setting up a render cluster for just the one Mac Pro.
Use Disk Warrior regularly. Drives have at least 25% free capacity, thanks for mentioning that.
I did use Disk Utility to repair permissions - there were several that needed it. Also 'Reset Background Processing' in Compressor, and downloaded and ran the free utlilty Compressor Repair. As a result, encoding the same lecture for DVD at best quality 90-minute took a much more normal 5 hours and 43 minutes.
Glad not to be looking at possible drive failure, even though I do keep drives backed up.
Once again, thanks for your suggestions. Much appreciated.