This might be my fault
further investigation and the use of mediainfo, some of my movies have aac 5.1 and some aac 2 channel. I know I used different software and different machines to rip, but some further research reveals that for iOS aac 2 channel should be first audio stream or the only audio stream.
I'm going to test this using handbrake on a film that is not streaming to the iPad.
Apologies for not researching this further....BTW VLC works great connecting to Plex on my nas.
It is indeed the audio, ripping a current iso using handbrake and selecting mp4 and including 2 audio channels, aac 2 channel and aac 5.1 for surround this will then play on VLC and on a PS3.
Using an mkv container on handbrake but selecting aac 5.1 the same movie will play Ok without any streaming issues, although I have a transcode folder set up in Plex I am not sure if the movie is transcoding on the fly, which it could well be as this same movie (mkv) plays on a PS3 but only 2 channels stereo.
Anyway at least I know what I have to do to sort out my streaming problem...
loadsa work.