Hi slingblade,
Our apologies for letting this question slip through the cracks unanswered.
The reference to stage 9 is an internal message. The underlying cause (exception) should be logged in slp.log, which can be accessed from SLP Code Protector via Tools|Show Log.
(At present, stage 9 refers to the writing the IL code back out after transformation. This may mean there is a problem with a particular construct in your code, or it may simply have been a file access error. I guess its too late to be sure given the time that has elapsed. Again, apologies for the delayed response, but hopefully this information may help someone else following in your trail.)