I'm wanting to do some transitions as a background to some green screen shots so as to give some subtle movement and change in the background.

So...I have 2 'cloud' scenes with 'clouds in different places. If I do a linear fade from one to the other over say 10 minutes, at the middle, the opacity of one is down half, while the other is up half, meaning there is a general lowering from full opacity at one end to the middle, and then a raising from half to full opacity from the middle to the end...with corresponding lightening at the middle. If I change colour from one end to the other a similar thing happens. Having two tracks at half opacity doesn't seem to add up to full opacity...though I guess it should...seeing the clouds are at different places, the clouds from each track are at half Opacity.

I would like to do the transition without this lowering then raising of opacity (although perhaps it could be part of the subtle movement and change).

Is there anyway to do this?

Sorry this isn't actually addressing your specific request, but have you considered using the Vegas Noise media generator (one of the cloud presets) and slowly adjusting the offset x value over time for some reasonably realistic moving cloud effects. Personally I think they are move effective if you set the background colour to transparent and lay it over the top of a still of a sky with some distant clouds, for added depth.

Put the videos on 2 separate tracks, and fade out the video on the upper track, revealing the lower track

Put the videos on 2 separate tracks, and fade out the video on the upper track, revealing the lower trackOf course!! Thanks so much. Exactly what I needed. Appreciated.

Sure, glad I could help :)

Once your videos are on two tracks, you could also play around with the different composite modes to see if you can improve the effect - eg you night be able to have the just the white clouds (and not the blue sky) of the 2nd track creep in at first, so that the clouds mix together more subtly without having a blue tint over them from the patrially transparent blue sky.

Once your videos are on two tracks, you could also play around with the different composite modes to see if you can improve the effect - eg you night be able to have the just the white clouds (and not the blue sky) of the 2nd track creep in at first, so that the clouds mix together more subtly without having a blue tint over them from the patrially transparent blue sky.When I refer to 'clouds' they're not 'clouds in the sky' but a Photoshop generated cloud background as per Create A Portrait Studio Background - Photoshop Tutorial (http://www.photoshopessentials.com/photo-effects/studio-background/)

I'm putting a gradient across it so I can have it light at the left hand side for illustrations I'm going to use...and then I put a colour gradient across it to add zing to it...well something more than grey anyway...see below. I will be in front of the coloured area. Both the clouds and the colour will change over perhaps 10>15 mins, and with some of the sessions which are longer ... 15>25 mins...I may put another cloud and colour at the midway point.