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There's a long and silly reason as for why this is a problem.
The short answer is that Unity renders depth separately for each shader, by reading a special shader file that has a bunch of tags in them. Based on which tag your shader has, it will use one of those to render depth. So what you need to do, is to download Unity's builtin shaders, find the shader with the depth passes (I forgot the name of it), and then add your own shader to it by hand, rendering only depth, and make sure that the tags match, so that it will use that shader for depth rendering. You'll have to do this for every shader that has custom depth behavior, which is a bit of a mess
I usually only expose those things that Unity provide natively in their shader code, and I believe this isn't one of them. You might be able to do this on the C# end, passing in offsets in the TilingOffset parameter of the texture properties, or by mapping it in world space or object space, rather than UV space.
For now you can flip it manually using the oneminus node on the V channel, and then appending back the U channel and the modified V channel
Try this reinstall procedure: http://acegikmo.com/shaderforge/faq/?Q=erroronnewversion#erroronnewversion
Pretty sure I recompiled them before upload. Did you do a clean install? (Delete SF before importing the new version)
There's no way to prevent SF from overwriting the code at the moment I'm afraid
Kundesupport af UserEcho
You'll need to be running Unity 5.3 for the latest version of SF :)
Full version info here: http://acegikmo.com/shaderforge/changelog/