By default Zbrush can't bake matcap to diffuse map. Here is a link to plugin: http://www.zbrushcentral.com/showthread.php?170886-MatCap-Baker!-unofficial-Information-Installation
Sounds like reversed normals. Try reversing them. If you have an alpha channel in any shaders, by default it connexts to transparency also, so it could be that.
Hey, they aren't mine as previously stated. They are from Ryse: Son of Rome and assets that come default in CRYENGINE. I'm changing them with my own soon.
Yes, I tried that, and there is no difference. Tried both compressed and uncompressed, the issue remains. I'm using the default scanline renderer, and Nitrous driver as the display driver.