I'm using Substance Painter, and for some reason, on this current model, I cannot paint over specific polygon faces.
Initially entire sides of the model could not be painted on, but I found out this was because they were mirrored and I had their UVs displaced off the main UV space for baking purposes.
So I fixed that by moving the UVs back, but specific faces (not even limited to ones that were originally mirrored and displaced) still cannot be painted on.
I've tested my model in other programs, and Painter is the only one having issues painting on it.
Here's an image of the texture I painted random lines over to illustrate. All the breaks you see are faces I can't paint over.
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It was happening in both 2D and 3D, and I was using Tangent and Object.
The color picker is uselessly inaccurate as well though, among other things, so for now I'm just done with Painter. Maybe a few versions from now it'll be worth using for hand painting textures and I'll give it another shot.