The Problem: We are experiencing disconnected RDP connections on handheld Motorola devices running Windows embedded, when connected wirelessly to the new Mikrotik cAP-ac units we installed in a large warehouse. Ping tests from my notebook through the cAP units to the gateway router result in very high jitter. Over several hundred pings, the ping results range from 1ms to over 1200ms. This is while my notebook is stationary and has an excellent signal to the nearest cAP.
Environment: 29 cAP-ac units have been installed in a very large 360,000 square foot warehouse. Each cAP is mounted about 4 foot below the correlated flat roof, spaced out throughout the warehouse. The roof is approximately 30 foot above the floor. In the warehouse there are 63 rows of skid racks. We have mounted cAP units on every other row.
Configuration: All cAP-ac units are centrally programmed using CapsMan, running on an RB3011 router. Only wlan1 is being used on each cAP and all cAP units broadcast the same SSID and use the same frequency. The 5ghz wlan interface is not being used at this time. DHCP client is enabled on the eth1 interface on each cAP. We initially had RouterOS version 6.43 running on both the CapsMan router and the cAP-ac units, but have upgraded to 6.44, without any improvement.
Troubleshooting steps we have tried:
1) Did a wifi analysis and turned off all devices using 2.4ghz channel 1.
2) Confirmed that all cAP units were provisioned to use channel 1, 20mhz channel width. WPA2 encryption enabled.
3) Changed the channel used by the cAPs to 11, but no improvement.
4) Upgraded firmware to 6.44 on the CapsMan router and on about 1/3 of the cAP units closest to where I was running tests - no change.
5) Configured one of the cAP units as a stand alone AP, not configured by CapsMan and turned off the other cAP units in that end of the warehouse. Connections through the stand alone cAP had the same ping jitter problem.
6) Logged into one of the cAP units and ran pings to the local gateway IP. The results were less than 1ms consistently. This would seem to rule out a problem on the ethernet network.
7) Setup one of the cAP units away from the metal roof so that it was located about 15 feet off the floor, and then turned off the other cAP units in that area of the warehouse. We did this to test whether proximity to the flat correlated metal roof had anything to do with the ping jitter. Connected our test notebook over wifi, to the test cAP, 15 foot off the ground and it did not make any difference. Over 100 pings to the local gateway IP, times varied from 1 to 600ms.

I have included a screen capture of the wifi analysis, showing the cAP units assigned to channel 1 and other equipment assigned channel 6 or 11. I have also attached a screen capture of the ping test results, showing extremely high ping jitter, when pinging the local gateway IP, through the cAP units. A third screen capture shows the registration of my test notebook to the cAP nearest me. I am not sure what I need to do to get this wifi network providing stable connections. Any suggestions would be appreciated!