Hi Matchless.. I see a few things going on here.
1. check your page settings again. you say that fade option is checked on every scene. However this option is not found in Page settings.
In Page settings you will find channels. Every channel has a Fade option.
This fade option needs to be checked.
What type of fixtures are you using?
2. Patches in Compu Live 3D window are different than Patches on Compu Live program window.
If you have more than one page, then you will have conflicting issues.
I have never had fixtures reposition simply by saying yes. your supposed to say yes so that the channels of the Compu Live match the fixtures in 3D window. positions changing may have to do with your 3D problem.
3. All of you work for 3D easy view needs to be saved in the folders it asks. The software is written to look in those folders and not subfolders that you create.
When you work on 3D easy view, let everything save to its appropriate folders. When you save your 3D work, you can save this in a completely different folder. but while your working it. keep everything in the easyview data folders.