Feel free to continue the conversation here guys, if it's helpful to people.
I had another look at the WMF player again today and switched my method of working. I have now split the videos into smaller pieces (I was playing 3x12 minute videos but now I have around 18x1-3 minute clips - 3 of which are played simultaneously) and I am using the method mentioned by obviousjim here to play them back seamlessly. It seems so far to be a lot more stable.
This method works fine when playing back at a rate of 1 but when I speed up to 3 I get a very clear pause when the new videos starts to playback. Any ideas on removing that pause?