I seem to still be having the same (or at least, closely related) issue. It had been happening under the previous stable release, but I saw the notifications that it'd been fixed in the next beta, so I didn't report it at the time. However, I've just updated to the latest stable release (Version 3.0.5724.3) and am still experiencing the same issue.
Here's a rundown of what's happening.
On the "Upcoming" tab, there are a lot of shows missing. When I compare the results displayed on the Upcoming tab (which is missing things) with the results listed on the "MB Upcoming" Chrome extension (v0.1.7, which seems to be the complete list), it appears that the missing episodes are the first listed episode for every day (I've been tracking this for several weeks since noticing the problem, because the extension only displays 3 days of data at a time). The Emby Android app (v2.3.80) is having the exact same issue as the browser interface, always dropping the first listed show for each day.
So that means that on any given day, if there are two shows scheduled, I'll only see the second one. If there are four shows, I'll only see the second, third, and fourth. And when there's only one show scheduled for the day, the day doesn't even appear in the list.
Speaking as a programmer, my opinion is that it appears to be an array numbering issue, or something of that sort. If you're storing all of the shows into an array, and it's auto-numbering them as upcoming, upcoming, upcoming; but then you're retrieving them starting the keys at 1 instead of 0, that would explain all of the missing records. But I haven't seen the code, I'm just guessing based on previous experiences. ;-)
Hope this is helpful information, let me know if you need anything else from me and I'll be happy to provide what I can.