Does  ZBrush Face Tools features work when using own mesh different than basemesh?, have own mesh with fitting blendshape fitted to cc4 clend shape standard naming.

It needs the CC3+ base mesh (or later versions). For custom characters you could use tools like the Headshoot 2 plugin to transfer the geometry of the head to the CC3+ mesh.

It could also work with external tools like Faceform Wrap, which can transfer complete characters, not only the the head. But I cannot say that for sure. 

Has anyone encountered such bug? When I'm sending any mesh from CC to Zb via face tools it come with flipped UVs (so all displacement is applied wrong and textures look flipped) It seems to me that head comes in flipped upside down also, which may cause all the trouble, but I'm not sure. I guess that flipping UV's is just And I didn't find any options or preferences that might cause it. Any thoughts how can I fix it?