Screen Aspect ratio
There should be no need to change anything other than the resolution of your monitors if you are working on a two monitor set up at both locations. I think the res at Suttie is 1024 x768 or with the matrox added 2048×768. This is a 4×3 format to match the projection surface.
You environmental vars should be set to match the projection screen surface physical dimensions of height 1.8 and width 2.4. Screen distance is the distance to approx the first row of seats but as changing it will affect positioning of objects on screen I keep this set to 2.5.
Changing from the above values will have a serious impact on the stereo… and therefore is best avoided.
So the solution to you problem? Is there a config file being used as well as these envs? This could be the issue.
Alternatively put “stereo” to off down at Kings and just work on a single monitor…. but I work on a series of different setup's with laptops and desktop machines all driving two monitors and have no need to change the above standard figures…. have even driven an imax with no change!
Alpha on PNG format image sequences
Png with alpha works fine in Quicktime, it is what we use for images and movies. But not sure what Blender is exporting, there are png options…. have you tried taking through photoshop?
On NOT using paths
You could spend and will spend days trying to get paths to do anything fancy… much better to use multiple slides … captured movie of live animation finish in matching position of the following interactive slide…. etc … if you are using paths then there is virtually no difference between this and a movie to the viewer… and by using the autorun feature you can make this transition from automated (movie) to interactive seemless. This is how we are doing much more of our content.. as it simplifies the presenters job.