The AP = Ubiquiti Outdoor AP Plus. Latest controller and firmware on the AP
Nano's are all NanoStation M5's - all now running V6 firmware.
All Cat5 cables are factory produced, we do not make any cables ourselves.
The switch is definitely auto negotiate, i have to presume the AP is as i do not know of any way to alter this and looking at the UBNT forums everybody is pretty much saying there is no way to change it either ( although i expect its possible via SSH which i haven't done ). Just to note, when installing the AP's are taken from the unopened box, mounted to the column and powered up via POE. when the network is up and running they are adopted into our cloud controller and the site config takes over.
I have ran a cable test which has proved to be interesting, the results are below..
And when i first saw then i was concerned that i had bad cables... but we are getting the same port state change on every switch.. so i ran the cable test on every switch... and got the same result on every switch... I also ran it on some of the ports running the Nano's... got the same result every time i ran the test.
The pair length has to be incorrect as i installed all this kit and i know for a fact that the fly leads connecting the kit to the switch are 1mtr, in fact some are only 0.5. It also suggest that only two of the pairs within the same cable are different lengths... With this in mind I'm not sure the other results of bad cable and short status are correct either

Finally... regarding cables, taking into account every fly lead we use if factory produced, as we are getting the same error on every switch... on a single port in the main ( a little on others ) ... i can't believe its a cable problem
So moving on.. found something odd... looking at the logs on all switches this morning... all the switches that are slightly away from the main town area stopped reporting an issue around 8:30 pm ( GMT )... the two that are right in the town center stopped reporting issues around 9:30pm
Nothing has changed other that the one switch has had a firmware upgrade but that was later at around 10:30 pm from memory, so i am presume the logs stopped due to inactivity of client connections which is very likely as this location is not very busy, especially at night.
I will keep my eye on it throughout the day and let you have an update after lunch when i know the town would have been much busier.
In the mean time any info re the cable test would be appreciated. I may grab a new switch from stock, couple of Nanos and AP and set it up in the office to see what cable test i get from that.
Thanks for your help so far.