From looking at this, it appears that on the "websites" scene the GGA_shows element is appearing when this scene loads in eNVy_home_ 5-10.hype.zip. This is what I would expect given the animation. First, the element itself doesn't have any Flexible Layout settings, so it will appear at a different position than the other elements above it that do. Beyond this, you have an opacity animation, but the first keyframe starts at 100%, meaning any time before will also be that opaque. The subsequent keyframes are 99% and then stacked underneath that is 0%.
Opening the document in v3.6.2 has the same animations, and your eNVy_home_ 5-8.hype.zip looks the same to me in the later v3.6.3.
Is this the issue you are seeing? If not, I'd appreciate if you could perhaps elaborate on the problem with a screen capture using QuickTime Player's 'File > New Screen Recording'.