This happens if you use monotone partitioning, which is fine for small tile sizes but its practically useless for large tiles. See this blog post Digesting Duck: Monotone Regions
To "fix" that, watershed partitioning can be used, which is the default now anyway, I think.
(I noticed you've been looking to build your own Recast. Could you elaborate on the simplifications and improvements that can be made when specializing on WoW? I remember pendras thread, but I never understood why his system would perform magnitudes faster than Recast)