Transparency flickering between custom unlit objects

I've been having loads of problems with transparency when using multiple shader forge built materials. 9 times out of 10, I have no issues when rendering against the standard unity shader.

After failing to get the effect I was looking for using normal transparency, I opted to use the system I currently have to render faux transparency. I'm still getting issues though, and I can't figure out why.

It's hard to explain what I'm talking about without images/video, so here's a video.

http://files.1337upload.net/transparency-dd8ad8.mp4

(Warning, it's a huge file)

And here are the two shaders involved.

This is for landmasses:

This is for the "Ocean":

There is a lot more, but it all boils down to a single emission value.

At the end of the day, it's just 2 unlit materials with an emission output. I don't understand why it has so much trouble.