There's an issue with pixel scaling specifically on the "gbc-5x.slangp" shader. Other shader files of the same type, such as 4x/6x, do not have this issue.
Tested this with both Sameboy and Gambatte core.
Tested this in both glcore and vulkan video driver.
Same results.
When using gl as video driver, the glsl shader "gbc-5x.glslp" works fine in comparison.
Had this problem for many months so retroarch version does not seem to matter.

PC specs:
CPU: Intel Core i7-4770K
GPU: GeForce GTX 770
OS: Windows 7 x64

Screenshot examples below:

gbc-5x.slangp shader:

gbc-5x.glslp shader:

gbc-5x.slangp shader:

gbc-5x.glslp shader: