Ok these MP4 files are working prefectly now. I found I actually did already have the latest version of Haali installed - but when I had installed it I had unchecked all the optional things like OGG, MPEG-TS...and MP4. In other words I only wanted H264 support for MKV files.
Installing it again, but this time leaving MP4 checked, is what got things working correctly. So now Haali is being used as the splitter for MP4 files - gawd knows what was doing them before! I never had a problem with the video quality - I use the Cyberlink H264/AVC decoder and it's fine.
So happy that Dolby pro-logic is still intact in the AAC audio, so now using ffdshow for the audio I have surround-sound again. (Windows MC has no pro-logic decoder so was limited to stereo only on the MP4 files with AAC audio).
Still don't understand what a splitter does, but now it's working guess it does not matter :-)
Lounge Gigabyte 780g-Nvidia GTX560ti-AMD PhenomII 960T-Crucial C300 SSD 64gb-Samsung F1 500gb-2x Samsung F1 1tb-NovaT USB-Nova HDS2-XP Pro/W7 (dual-boot).
Gigabit networked to:
Gigabyte 740g-Nvidia 8800GTS-AMD X2 6000-Samsung F1 1tb-Seagate 320gb-Samsung F3 1tb-NovaT PCI-TBS 6981-XP Pro/W7 (dual-boot)