Trig,

Found some old tips on this.

Delete the User Preferences

You can resolve many issues by restoring Compressor back to its original settings. This will not impact your project files. To reset your Compressor user preference settings to their original state, do the following:
In the Finder, go to ~/Library/Preferences—the tilde (~) represents your Home folder.
Remove the following files from the Preferences folder:
com.apple.Compressor.CompressorSharedService.plist
com.apple.compressor.Compressor.plist
Note: This will not delete any custom settings that you may have created. Custom settings are stored in ~/Library/Application Support/Compressor.

Repair File Permissions
Close all the files and applications that you have open.
Open Disk Utility (located in the Utilities folder in Applications) and select your startup disk in the list on the left.
Click First Aid.
Click the Repair Disk Permissions button.


Remove and reinstall Compressor

To reinstall Compressor effectively, you need to remove the application, its receipts and associated files, then install Compressor and use Software Update to install additional updates. Follow the steps below to completely reinstall a fresh copy of Compressor. Note: Make sure that you have the installation discs for the application that Compressor was bundled with and the serial number handy before starting this.
Use Finder to remove the following listed items:
/Applications/Apple Qadministrator.app
/Applications/Apple Qmaster.app
/Applications/Compressor.app
/Applications/Utilities/Batch Monitor.app
/Library/Application Support/Apple Qmaster (the folder)
/Library/Frameworks/AECore.framework
/Library/Frameworks/Compressor.framework
/Library/Frameworks/MediaServerAPI.framework
/Library/Frameworks/Qmaster.framework
/Library/Logs/Qmaster (the folder)
/Library/PreferencePanes/Apple Qmaster.prefPane
/Library/Receipts/Compressor.pkg
/Library/Receipts/Qmaster.pkg
/Library/Receipts/Qmaster_Frameworks.pkg
/Library/StartupItems/Qmaster (the folder)
In Finder, choose Go > Go to Folder.
Type the following path:
/usr/sbin/
Click the Go button.
Locate the following items from that Finder folder, and drag them to the Trash: 
qmasterca
qmasterd
qmasterprefs
qmasterqd
In Finder, choose Go > Go to Folder.
Type the following path:
/var/spool/qmaster/
Click the Go button.
If there are any folders inside the qmaster directory, drag them to the Trash.
From your install disc, reinstall Compressor and Apple Qmaster.
When finished, use Software Update (under the Apple menu) to update your software to the latest version.

Hi Trig,

Good to hear that you got it up and running.

--ken