I can confirm this behaviour with Textra and Missed it! 4.3 beta 2 too.I realize this was an older post, but I just experienced a similar problem on 4.4 - had Textra selected as my default SMS, and missed messages wouldn't register in the counter. If I changed the default SMS to stock android messaging, it picked them up. I made sure the listening events was checked, but no go. I had to add Textra as a monitored app and delete the missed messages entry and it started working. Calls and gmails worked fine.
I noticed that it is investigated nearly for 9 months by developer: https://plus.google.com/110589031691310378791/posts/DpoZDAbqL7m
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