Alpha:fade shader and Skybox?

I've made a shader for a custom procedural mesh and I can't seem to get it to work right. At certain distances and angles the mesh will disappear and reappear when the camera moves on. It doesn't just happen from very close or very far and I've modified the camera clipping plane settings just to be sure, so I don't think that's it. What research I've been able to do has mentioned some issues with Skyboxes and clipping but I'm not sure how I would resolve that. The Skybox shader already has Cull and ZWrite off so I don't know what else I could do on that end and turning ZWrite on in my shader didn't seem to work. Has anyone come across this before or have an idea about how to solve it?