Thanks for contacting us. I have two suggestions:
1. Please make sure you have defined a boarder layer for each job that will be included in the panel. Without it FAB 3000 must use the overall extents for each job. Here's a forum post that may be helpful
2. Feel free to save and send me a sample FAB 3000 workspace file (*.wrk). I'll be happy to take a look and instantly determine the cause of any problem.
Please note, the above links have been updated. Please use the links below.
FAB 3000 Panelize - Full Video
Panelize Gerber files from Eagle PCB using FAB 3000
FAB 3000 Panelize Single and Multiple PCBs. Save 33% Costs.
FAB 3000 Matrix to automatically panelize from a single import.
Need to Panelize 40 different PCB's at once. Can you help? (includes Manual Placement (Snap and Add Insert)