Just a quick update on this, as you all may know I fixed the WIFI transfer speed problem. However, the random disconnection problem remained. This would happen on both WIFI and wired LAN, and was not easily reproducible. It seemed to be completely random, I spent an entire evening trying to diagnose it to no end. I tried transferring the same batch of images over and over and it would not fail at any certain point or during any certain event/time/etc. Sometimes it would transfer 35 images before failing, sometimes less than 10. I could not make it fail at any certain time, it was only inevitable that it would eventually disconnect.
After coming to constant dead ends trying to diagnose it we started thinking outside the box...we had had problems at the studio before with a taxi office nearby whose radio transmissions used to interfere with our bluetooth mice, due to them using excessive RF power and a transmitter that was bleeding over frequencies etc, so we thought it may be something to do with that but we couldn't prove it.
Well I am glad to say that on Wednesday night we finally found out why it was randomly disconnecting, and I am amazed that a £600 device would suffer from such a stupid flaw. It is the battery. As amazing as it may sound, the file transmitter does not function correctly if the battery is at 2 bars or less. I know, it's absolutely incredible. We finally realised this after I swapped the battery just prior to attempting to demonstrate it failing. And you would never believe it, it transferred an entire CF cards worth (~15GB) of images in a single go without disconnecting.
So in a nutshell, if the battery in the file transmitter falls to 2 bars or lower, it will carry on 'working' (as in it won't turn off), but it will not work in a stable fashion. I have no idea why this is, but I can now reproduce the problem every time.
I am really hoping Canon have fixed this in the upcoming firmware for the 5D Mark III. I am quite tempted to contact them but I know there is no way I am going to get through to anyone at their end who actually understands what a WFT-E7B is and doesn't tell me to flush my DNS or empty my recycle bin when I try to explain the problem. If you search Google for "WFT-E7B problem" or similar this forum thread is fairly high up on the first page of results so hopefully anyone having the same issue will come here and see this!