Hi Adam,
Is this an upgrade or new installation?
If an upgrade, one option you would have is to shutdown Eclipse, rename the /.codemix/engine folder to another location, and start it back up again. This will re-extract the Engine which may be having issues.
If this is a new installation, beyond the steps above, do you have any particular virus software in place? IIRC there is one Comodo that has caused issues in the past.