Richi,
First – just in case you weren’t aware, your files are safe and will be directly accessible from the file system in any event.
This message typically appears when CodeMix is installed into MyEclipse (even then, should not be easy to run into this). Can you tell us more about your installation – how and into what have you installed CodeMix? Please also send us your error log – this will help us figure out what is going wrong. You can find your error log at [workspace_location]/.metadata/.log
Hope to get you back up and running soon.