I'm having problems where whenever I log in or restart, OS X is asking me for my iCloud password and then telling me I need an app-specific password for Messages, even though Messages is logged in and iCloud is already working everywhere. When I put it in, it keeps asking for it, and I have to cancel the prompt multiple times before it disappears entirely. It's really frustrating me, and I have no idea what's causing this to happen. I was hoping the new beta would fix it, but I was wrong.
That's related to the new 2 step verification, try generating a new password via Safari. It's automatically generated, you need to copy and paste it. Had this problem on 10.10.3, it's so awful that apple own apps don't support 2 step verification -.-