I've seen this with a few suppliers, and I think it's just cost-cutting when printing (cheaper ink, and less ink used per target). WA have specific colours they tell suppliers to use when they print the targets, but even with targets that have a WA license number printed on them, I've found that cheaper ones tend to either arrive washed-out (or bleach at a hint of sunlight), and vary in colour intensity. There's a stack of three-spot targets at my club that no-one ever uses because the red is a light pink and the gold is almost white.
In my experience, I've found that JVD ones tend to keep their colour longest... Or at least long enough to get shot through and destroyed. There is a little variation batch-to-batch, but not enough to be easily noticed at the other end of a range.