When using GregTech Community Edition (GTCE) version 1.12.2-1.10.7.594 and VanillaFix version 1.0.10-150, the overlay animations on the GTCE blocks are frozen. GTCE doesn't have the animated textures on the blocks themselves, and instead uses an overlay on top of a base block. When the animations are triggered (usually by running a machine), they only show the first frame, and do not show any subsequent frames. This continues until the animation is set to turn off (when a machine stops running), where the overlay texture reverts back to another texture file (that is usually non-animated).

Another case is with the GTCE Cover System. It uses the same overlay system as above, except it has animations running at all times. They are almost always placed adjacent to another block, so they aren't visible most of the time. But when they are visible, they behave as above.

It can be technically "fixed" by setting the following config option to false:
B:textureFixes=false

However, this isn't really the best solution and many would also like to have the benefits of having the config option set to true.

I have the same problem, (using Omnifactory v1.2.2 with GTCE 1.12.2-1.8.4.419 and VanillaFix 1.0.10-150), I really hope it can be fixed.

I also thought about a list of mod names in the config to disable texture optimizations for, however I don't really know if this is possible, I'll try looking at the code of both VanillaFix and GTCE and figuring it out.

Note this is likely a CCLib incompatibility.