UV on Glass pan Top something is offset

Near impossible to see what you mean without the default resourcepack. Could you point out the error with the default one?

I can't, you have to use 32 pixel to see the problem correctly. The Default have almost pure white pixel all around corner, so we can't realy see the problem.
Look how the brown pixel is over the gray one,
Or Just look all other top corner, and compar to the one in circle.
The pixel should align all corectly, but that corner (just that one) is not align with the rest.

Please attach your resource pack (or the relevant parts)

Well mark this has resolve, i just realize i wasn't in 1.8 when i notice this problem, and it as been corrected since.
The other problem is the flickering on top of the glass because 2 texture overlay each other.