Can you look in the About FreeFlow Core dialog and make sure that the server and client versions match
Sometiimes silverlight is a bit too aggressive about caching content and the FFC client (the app that runs in your browser) does not update.
Please post a screenshot of your system.
Just installed 4.0.1.1 and I'm not seeing the additional dropdowns, is this limited to a particular license type?
Giving this a little more thought (I know - I JUST replied to your email).
First: Make sure you upgrade to v4.0.1.1 as it has some required changes in functionality.
The Resize node has the ability to use manifest data for the width and the height
So, resize the document using MAX variables and make sure Content Scaling is set to None.
The print ticket will use the PDF dimensions as the media size if there's no other media information so this should allow you do use a single queue for any press sheet size.
As for the plex, you will have to use routing to select between Printer Destinations with a default job ticket set to the required plex. The PDF dimensions will drive the media selection as long as the main stock selection is left to Printer's Default.
Alternatively, you would add a script to the HF to pull the two attributes from the CSV and create an XPIF with the required press sheet size and plex.
