Thanks Kevin. Reading your post does make me think we share a similar problem i.e. parameters getting recording into cues (or elsewhere) when they shouldn't be (or shouldn't be expected to be).
I've got an even weirder discovery from this morning. I loaded quite an old show that I knew had working submasters (that work ontop of other cues). Once the OS had converted the old show (from back when submasters were submasters), the converted Playbacks actually work as expected (for example, I have several that just set the colour of all the movers to a single colour, red, blue, green etc. and these work fine without affecting position, effects etc.) but if I try to program the same Playback from scratch they don't work and instead seem to contain position/effects information too where I don't want it.