I did not follow the old link, but this is probably normal and expected behavior.
Zones are calculated by an algorithm, and those keep a defined clearance from any tracks and pads that are in the zone. If there are area’s where you do not want tracks to be routed, then use: PCB Editor / Place / Add Rule Area, and then set it to: Keep out tracks. I do not use freerouter myself, and I do not know if that program is aware of and respects those keep out area’s.