The fix to this problem is actually quite simple!
I am indebted to the person to spent time looking into this and inevitably now owe them beer!
The CLEO module is stored in moodle/local. Copy the file:
moodle/local/lang/en_utf8/cleo_mis.php
to the path:
moodle/lang/en_utf8/
As Secretlife said, all the problem is is that Moodle is not able to load in the correct language file so the strings are not being loaded in correctly, hence the odd variable names. Really, this could be added as the final step to setting up CLEO since it looks like Moodle has changed something?
