Yes, a screen capture would help us to understand your problem. We cannot understand the problem without seeing a screen capture. Probably, we would need to look at your UV map as well. If you cannot post images of these, try to create a zip file with these images, and place it on Dropbox or some location where we can download it and look at the images.
Typically, when you have problems in Substance Painter is "IS" because there is an error in the UV map. The error you are describing is not caused by vertex colors or materials. The most common kind of error is an overlap of one or more "shells" in the UV map. That is, an overlap in the individual pieces.