The only way may be to open one of the books in question to find out what it is. But, I can tell you I've known about the extra blood spot in the logo for years and it is an easy way to spot a 3rd printing at a distance.
The interiors of #1's are also slightly different. A lesser known fact is that each if the first three printings is a slightly different size (as are the 1st and 2nd printings of #2). I believe the 3rd printing is actually more narrow than a 1st printing. And, the interior grey tones on the 3rd printing are more washed out than the 1st and 2nd printings. These are some additional things to look for if you were to authenticate a 1st printing and didn't want to rely only on the cover.
I think that owners of these books should work with CGC to help solve this mystery. We're all speculating until someone can examine them in more detail. If someone has tampered with one of the CGC cases, CGC should be able to inspect it first hand and confirm this. If the owners crack open the cases themselves, we may never get to the bottom of things. But, I think it's important that the results be shared publicly so that people can be assured that they have a first printing inside books that are certified.
So what's the final verdict on this? Are those for sure misidentified 3rd prints?
I hope someone from CGC can weigh in on this, because I'm currently shopping for a 1st print and I'm putting a lot of trust in their slab.