I've noticed that, too, at least, at the CLEVNET library. I didn't really look at old titles, but when the September change went into place, I didn't notice any new books not being available in both formats. Then, after Penguin temporarily withdrew its support for Kindle ebooks at the library, I began noticing it on new books from then on. And it's not just Penguin - I've seen it on Harlequin ebooks that only ePub is available.
Now...that MIGHT be because Harlequin makes ePubs available on its own website a month earlier than it releases to other sites, so maybe only ePub was available when the library pre-ordered the books. I haven't gone back to see if Kindle links showed up after the first month.