I always just open production manager and add the files to it and then print or cut etc.
Make sure your default settings are not for print only. Not sure if going through Flexi first will over ride the settings in production manager or not.
Just to confirm what you are saying: When you sent a file that is a print and cut, it just prints the file but does not cut? Is this right?
Or are you trying to send a file that has already been printed and then you take it out, laminate or whatever, and put back in to cut?