Hi Barb,
How have you configured the tray calls? Are you specifying a tray for each page, and it's not picking some of them, or is it all set to "Auto-Detect"?
If it's all set to Auto-Detect, well, the tray calls will be handled in whatever way the printer decides to handle postscript-based tray calls. Since it's pure postscript, you may get a different behavior than printing from Word(which uses the windows driver), and each printer has their own postscript interpreters and result can vary from printer to printer. So we don't really have much control over this.
If you have set specific trays, and it's ignoring some of them, then it could be related to the PPD that you are using. Make sure you are using a PPD file made for your printer instead of the default PPD, as the default PPD might not contain the proper information on the trays and other features.
Regards,
Raphaël Lalonde Lefebvre