Most likely a bug with gerber generation in Altium Designer. I have stumbled upon similar bug with PADS in the past, some 2007.x-version, gerber generation failed to generate proper outline for fill polygon. I caught it with CAM350, I always check gerbers and do a netlist comparison against IPC-D356A netlist. For this reason, I often generate gerbers with drawn fills, even if it produces hugely larger files but no errors with fills.
Can you post the actual gerber file in question, I can check it with CAM350 (often used by PCB manufacturers)?
Regards,
Janne