PW was the first to notice that Google isn't letting bookstores join the affiliate program anymore. They're reporting that several booksellers cannot get in. A little bit of digging has revealed that this has been going on for nearly a month, with at least one website owner (it's not clear what type of site he has) attempting to join the program on 28 January. He couldn't get in.
There's even been an official response from Google that, while vague, does confirm the situation.
The Google eBooks program is currently not accepting new applications at this time. Thank you for contacting us and pointing out the directions on the page
It's not clear from my viewpoint exactly why Google closed just the one affiliate program - but not any of the others. Does anyone know what is going on?
Update: In what cannot be coincidence, I just got an email from Google about my Adsense account. They're making a number of changes to their policies, and I'm betting that the Google eBookstore issue is directly related. If anyone gets an email in the next couple days about your gBooks affiliate status, please let me know. It's going to be interesting.