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
http://forums.numericalinnovations.com/post/every-time-when-i-try-paneizing-the-boards-seem-to-be-placed-wrongly-could-you-6676770?highlight=merge+wizard
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
https://vimeo.com/157978225
Panelize Gerber files from Eagle PCB using FAB 3000
https://www.youtube.com/watch?v=46BbmW-14Gs
FAB 3000 Panelize Single and Multiple PCBs. Save 33% Costs.
https://www.youtube.com/watch?v=U167fe0vEmw
FAB 3000 Matrix to automatically panelize from a single import.
https://numericalinnovations.freshdesk.com/support/discussions/topics/14000002866
Need to Panelize 40 different PCB's at once. Can you help? (includes Manual Placement (Snap and Add Insert)
https://numericalinnovations.freshdesk.com/support/discussions/topics/14000010294
Numerical Support Team