There isn't much difference between regular and 360 video editing, other then the projection. And definitely not when it comes to things like transparency.
I would have to check it in 15, but in 16, make sure the PNG's are in the top (well, bottom in the timeline) layer, so like Ynotfish says in higher number tracks. Can it be you have FX tracks over the top (bottom in timeline) of your video?
I noticed the same thing, also fading shadows in PNG that became solid bands. I found that re-ordering the track down, below the fx track(s) in the timeline, the issue was resolved and PNG's look like they should.
Does this help you out as well?
regards, Frank