reflow oven issues with RO4003 PCB
We've played this game with a batch quartz oven with awful results.  To see what's really going on, instrument a pcb with a matrix of thermocouples and monitor the temps.  Chances are, you won't like the results.

Keep running tests, changing one variable at a time, until you get better results.

Things you can change:


Profile times and temps.  There is probably a solution, but you have to find it.  Try to align recorded temps with the published reflow profiles from the pcb/component manufacturers.
PCB position on the tray.  Use the thermocouples to detect hot-spots, move the pcb to find the most-even temperature area.
Adjust the Convection air flow.


Off course, all of these adjustments are interacting, so this procedure is a real PITA.  There's no easy way to go through this, except step-by-step.  Once you get a 'feel' for your oven performance, and different PCB's, then it gets easier but process never becomes 'Automatic'.

Good luck!