I created a new plot instead a territory like normal. The player was not able to build in it after I added them. After setting the priority of the plot region to 1 (higher than the territory priority of 0) it worked fine for him and he could build in his plot then.

I've never had an issue with priorities when there was already a parent-child relationship.

• Is the parent of the plot still the territory?
• Are there any flags or unusual members on the global region?
• Are there any other overlapping WorldGuard (not necessarily MCTowns) regions?

Yeah I think you're right, there was some overlap from another plot clipping some of it. Should've spotted it sooner, thanks!