I submitted a bug report to Apple Developer Bug Reporting on this on 3/11/2014, over a year ago. On 3/14/2014 I got a response stating that this bug report is a duplicate of another issue and would be closed. So evidently someone inside/outside of Apple had already submitted a similar request. However, with all the releases we've seen since then, they have not fixed the issue. Here are the "steps to reproduce" that I submitted originally:
1 flag an email in inbox.
2 go to flag folder to confirm email shows up.
3 flag an email in another folder, not inbox.
4 go to flag folder, only inbox flag emails appear.
I wonder if a) they actually understand the nature of the defect, and b) if their defect queue and prioritization keep pushing this issue to the bottom of the list. Either way, I would have expected that it got into a production release by now.