I tried emailing Arturia support but got a fairly generic response about doing a factory reset and re-loading the latest firmware. I was skeptical but tried just for the heck of it, and it didn't change the behavior. I am glad to hear someone else is seeing the same thing.
After spending more time with it, here’s what I think is going on:
When you use the “step skip” feature, it loops your current pattern four times, no matter how long it is. Each “page” button (the “16”, “32”, “48”, and “64”) controls whether the step is skipped in one of the loops: if “16” is off, it’s skipped in the first loop. If “32” is turned off, it skips in the second loop. And so on.
If the pattern is 16 steps, it acts like a 64-step sequence where each page is the same, and it more or less behaves the way it’s described in the documentation because the second loop/page is controlled by the "32" button, the third loop/page is "48", and the fourth is "64".
If the pattern is 64 steps, it gets a bit confusing. If you are on page 1 and always want a step to be skipped on that page, then hold down the step button and turn off all four page buttons (“16”, “32”, “48”, and “64”). Then that step will never pay on that page. Otherwise you are just skipping it for one of the four loops of the entire 64-step pattern, which allows you to create 256-step patterns. So let’s say you hold down step 1 and only turn off the “64” button. Then step 1 will play three times in a row the first three loops of the pattern, skip on the fourth repetition of the pattern (on step 193), and then start the 256-step sequence over on the fifth repetition.
It’s hard to describe in writing, but hopefully that makes sense.
I can come to terms with this behavior if I practice with it more. My concern is whether Arturia actually intends for this to be the behavior, since it’s not clearly documented. It's fairly unintuitive IMO, and I could see them deciding to change it in a future firmware update if it's deemed a bug (which I thought it was at first). In any case, I’m just going to roll with it and try to learn how to use it to my advantage. It should make for some interesting drum patterns.