Troubleshooting wireless connection problem / site survey?

If you are using 2.4Ghz WLAN protocols then Channels 1,2 & 3 are too close to be used in a cell type layout like this. You want to use Channels 1,6 & 11 - Cisco have a good explanation of the issues in this article on the 2.4Ghz channel overlap problem and cell coverage strategies.

The primary effect of having channel overlap is poor throughput but the secondary effect will be that the various WLAN auto connect\zero-config services on your client PC's will be much more likely to drop an active connection and attempt to connect to an alternate. This behavior has been significantly improved in recent OS's but anything older than Windows 7 or recent OSX is likely to require some work tuning the client NIC settings to work optimally in a large distributed office WLAN like this if the channels are not widely separated. One other common source of trouble that I've come across were incompatibilities between the access point firmware and the client WLAN NIC settings - things like power management (aka CAM, Continuously Aware Mode) caused issues between early Intel Centrino WLAN adaptors and Cisco infrastructure that caused similar issues to those you describe. That issue was resolved years ago but there have been others and it's worth checking that there are no known issues with your specific client WiFi adapters and your AP's.

Things are much better in terms of the number of channels and the separation between channels in the 5Ghz spectrum - if your infrastructure supports 5Ghz 802.11n\a and the clients support it then set 5Ghz 802.11n as the preferred option for clients (or 802.11a which is only 5Ghz).

One other thing that is worth remembering is that there is a lot of junk in the 2.4Ghz spectrum. Try to get a basic spectrum analyser in to check that there isn't some other ambient noise source leaking into your environment, that can cause the sort of symptoms you describe too.