Just in case it helps any other forum members............................I have been messaging gazfocus for a week or more now as I also experienced a very similar problem. We have both been printing mugs over the last week or so (multiple suppliers/sizes) to see if we can eliminate the problem, which it now looks like we have. It looks like the problem comes from:
1.) Mugs not being perfectly straight (are any?)
2.) The paper not making good enough contact with the mug
It turns out that both gazfocus and I printed our transfers 3UP on an A4 sheet. I was using Truepix paper and he was using srace, which he cut down to be A4. In both instances we printed 3UP, so the paper was 210mm wide. I noticed that the A4 TruePix was Short Grain (i.e. the grain ran with the short edge), as a result the paper is more rigid when taped to the mug than if it was cut across the grain and folded with the grain. We have both been printing the opposite way around (i.e. printing 2UP on A4) for a week and the problem has been eliminated. I'm guessing the paper can "get into" the dips in the mug more easily if the grain follows around the mug. It's only quite a slight difference but it looks like it is enough to cause "a handful of problems" in an oven load of mugs. I'm guessing a similar thing might be possible with lighter papers, but I haven't tried that.
So if you print 3UP, get some mugs which are not as perfect as you might like, I'd suggest trying to print your transfers so you cut through the grain. Just to be clear this is really only an issue with printing mugs in an oven (as I guess the press would allow for this small difference more easily than a mug wrap) and only if the tension in your wraps is not sufficient to overcome the resistance from the paper. It looks like it can be a small but material difference between an oven load that's perfect every time and having a binned mug or two in a batch.