Ask any avid stamp collector about watermarked paper and this is what they will tell you: firstly watermarks have nothing to do with what is eventually printed on the paper. They are created by making a physical impression of a specific design while the paper is still wet. These impressions can be vary from the large and obvious, to smaller ones that can be seen by holding the paper up to the light to those requiring special wetting agents to see definitively.
If someone is saying that some appear different because of the machine they were printed with, they are lying or ignorant. My bet is they are lying. I would also bet that under examination these ballots will show that the alleged watermarks are actually printed on the paper.