@jamiewgrant 

My quick question would be that when you mention the speed dropping to 100, is this the NIC card reconnects at 100 or does the througput drop to that?

If its the NIC card try forcing 1000 rather than autodetecting, if its throughput then you have another problem

My concern is that everything in Yellow is running off one 1GB port in reality, namely the trunk marked in RED

3 DECO devices, 4 LAN and however many wifi is a real bottleneck on that 1GB port.    If the 16 and 5 ports support 2.5 / 5 or 10GB then that would be a good idea, if not i would consider that. 

My next course of action would be iperf3 tests at the following points.. test this when full speed and speed drops at the following points and compare

Please excuse the paint scribbles :)   X to X    Y to Y and  Z  to Z   get a baseline, then when speed is crap rerun the iperf3 test using a laptop straight to socket/patch or switch.. dont use WiFi..    gut feeling is X to X will stay same and other 2 drop..

This is probably your best course of action to investigate this.  If new switches is a possibility, check this first and look to 2.5GB ports on teh new stuff coming out.  It will run ok on 5e also

@Philbert thanks for the suggestions.

The NIC negotiated speed doesn't change on any of the three affected devices. Stays at 1Gbps. So it's the throughput that drops to 100Mbps.

I agree it's a bottleneck on that one socket, I've been thinking about upgrading it, but I'm not sure it would account for an intermittent problem - which is immediately fixed by resetting a switch. I've also tried running single devices through the switch and it has the same issue.

I have to admit to being a complete n00b when it comes to networking. Apologies. Is the tool you described easy enough to pick up and learn?

@jamiewgrant 

Yeah the tool is pretty easy to use.  Just download the files for IPERF3 and place on 2x devices connected to the switches mentioned, this will flood the connection for ~30secs and give you the result in mbps.   Ideally 2x laptops or desktops with at least 1GB cards.  One device will be a server other client, run the test and get average then swop roles round

To do this open command prmpt and run the following commands

on device to be server

iperf3 -s

on the client device 

iperf3 –c x.x.x.x –w 2m –t 30s –i 1s

x.x.x.x being the IP of the server..   as said do it both ways and record results.   test using   X  Y  and Z mentioned earlier

this will give you the actual throughput on the wire, get a baseline and run it again once the issue happens

upload the results for us to consider :)