Update: On Friday, Microsoft had me disable all of my inbox rules, just to make sure that none of those were interfering with Focused Inbox processing. They're also suspicious of our Ironport appliances and how they may be altering incoming mail, but that doesn't really make sense to me, since Focused Inbox is working normally for a co-worker and his mail goes through the same appliance. It will modify the Subject line to flag certain messages as "Marketing" or "Potential Spam", but it's been doing that all along, including back when Focused Inbox processing was working properly for me. The latest word is that I sent them a few sample emails that went to the Focused tab but should have gone to the Other tab, and I'm waiting for their feedback. As of this morning, I'd say it's half-working. Of the two dozen emails I've received that are not important (spam or bulk emails that got past the Ironport's filters), about half have gone to the Other tab and the rest showed up in the Focused tab. I even went so far as to clear out my safe senders and safe recipients lists (did that on Monday, actually).
In my opinion (which I may have mentioned before) the Focused Inbox "learning" process needs to have a reset switch that clears out everything and let's it start learning from scratch again. I don't want to have to do this sort of troubleshooting for any of our end users. I was very impressed with how well Clutter worked, but my transition to Focused Inbox has not been a pleasant experience. And I really miss my inbox rules, many of which moved messages into custom folders and kept my inbox pretty clean. I guess that's the price of being an early adopter.