FreeForm does not understand conditional layout commands. Creo VPS, FreeForm2, Optimized Postscript, PPML, VIPP do understand conditional layout commands.
You will have to use Optimized Postscript technology for the separator page.
Add an additional blank page to the job.
In the Layout Condition for this page, you would write an IF function to use the Tray ID or Tray Separator fields from the d-base to trigger when this blank (insert) page will be printed.
If you need more specfics, please email support@printshopmail.com. We can help you with the script/formula that works for your d-base file.