I know this has been reported elsewhere, but my experience is slightly different. I have an iPhone 5, and three mail accounts: iCloud, Exchange and Gmail. I have 8 emails flagged on my iMac at work. 4 are from my Exchange account, and have been "filed" in various subfolders, and 4 are from my iCloud account -again these have been filed in various mail folders. My iMac at home also shows these 8 flagged emails correctly (as did my iPhone 4). However my iPhone 6 is just showing one flagged email (it's one of the Exchange account ones). I can see no rhyme or reason for why this email shows as flagged but the others don't.
For the record, none of these emails are in my inbox any more. Also, following advice in another thread, I checked the the domain settings in iOS 6 > Settings > Mail, Contacts, Calendars > Account > Domain, and that is filled in correctly.
For the record, none of these emails are in my inbox any more. Also, following advice in another thread, I checked the the domain settings in iOS 6 > Settings > Mail, Contacts, Calendars > Account > Domain, and that is filled in correctly.