We have Ruckus ZF7263's at our hotel. Our vendor installed the APs with the auto configuration for channel settings. After doing a wireless survey I noticed that there were several adjacent APs assigned to the same channel. It seems from this observation that the auto assignment of channels doesn't always do a good job of assigning the channels. Is there a reason why I would have 6 adjacent APs would be assigned to the same channel? It seems that Dynamic Frequency Selection isn't the ideal way to setup APs in high density locations. Is it your recommendation to manually configure the channels instead of relying on DFS?
The problem with using the manual 1, 6, 11 setup is that it's the same way everyone thinks, and those might turn out to be the most crowded channel. Also, suppose I'm running a baby monitor or microwave oven that spews non-802.11 noise down near channels 1-4. If that's the case, using channel 1 is a horrible idea and will encounter nothing but interference. In fact, in a clean environment, if you deploy 3 Ruckus's with ChannelFly next to each other, you'll find that they will settle on picking channels 1, 6, and 11. Just in the real world, you'll find that some channels simply are no good.
Setting access points near each other to the same channel probably has few issues if they are all lightly used. If they are heavily used, the "losing" AP(s) will notice a sudden decline in channel capacity (due to the winning AP emitting a lot of traffic on that channel) and they will switch away.
The bottom line is, ChannelFly's problem is not capacity or not being able to avoid interference — quite the opposite — that's the strong suit. ChannelFly is the equivalent of you switching channels and doing speed tests for all 11 channels (and more on 5GHz) every few hours and choosing the best channel.
The weakness with ChannelFly is that some clients react badly to channel switches, and either disconnect from the wifi temporarily or even stay disconnected and assume the wifi network is down.
Are you using standalone AP's or a ZoneDirector? You should be able to have logs from your clients that correlate reports of connectivity problems with what the clients are actually doing (e.g. is there a disconnection right after a ChannelFly switch? Are clients disconnecting regardless of ChannelFly? Are clients picking distant AP's instead of nearby ones?)
The right way to approach this problem is by looking at the logs and possibly asking clients for their MAC address or host name for when they are having trouble.