Firstly, thanks to Anthony - Can't believe I missed that one. While the way to flag messages is resolved for me now on my iCloud/Me account, the fact that none of my flags are reflected on my Exchange account is not, and sadly that is the account which I use for about 95% of my mails; it was really the only thing I really needed from iOS5 - All the rest is handy, but not critical. Selecting "Mark" on an Exchange message simply offers the option to mark as read - There's no flag option. If I select a message sent to my .me address, I get the mark as read option, as-well as flag.
So, I'm wondering if this is a setting server-side, or to do with the version of Exchange server being run, as there's nothing in the OS I can see in the way of options. I'm tempted to delete the account and re-create it, but waiting for it to download all those messages again (and potentially screw up syncing, which it has done in the past) is putting me right off the idea. I didn't have the calendars, to-dos or contacts set to sync with Exchange (never use them) so I tried turning them on, but no difference.
If anyone with a bit of Exchange knowledge has any input or ideas, I'd appreciate the help.
Cheers