I too have had similary printer issues. While it is currently working for us, it's hard to say exactly what the fix was. The script that I created currently uses the same printer for 3 prints, but from 3 different trays, and it was the same scenario you're describing, where FM would ignore the second and third settings and use the first for all the prints. We got it working either by configuring the script on a mac, or by using FM 10 (or perhaps both), but we don't really know what configuration it was that got it. We're just letting it be in hopes it keeps working (even though for some people, it has randomly stopped working).
Your other option is to look into the Change Printer plugin from Productive Computing. Please note that I have not used this plugin myself, so I dont' know if it will solve this problem. Still, it may be worth a shot.