Hmm. Some thoughts going through my mind. Maybe the system has calculated it's more optimal to have those APs re-using the same channels so that other APs that are also in hearing range but carrying a greater load can use the non-overlapping channels.
Personally - I have never used manual channel assignments. I'm not a fan of that approach. It is a static calculation that is done once, versus a dyanmically calculated system that can consider load on AP and loads that vary (such as by time of day), interfence that can come and go, available RF spectrum (which can vary by time of day because of neighbouring WiFi). Maybe manual assignment works ok in an envirnment with no interfence, constant non-moving loads, and where their are no other WiFi networks around.
What power levels are you using? Lower power levels will enable greater channel re-use (and encourage romaing).
Some power levels I have found good for dense deployments that offers great compatibility are: