Since posting this Ihave archived my mailbox which has reduced it from 2GB to about 800 MB. I did have growlmail and dockstar addons running so I uninstalled them.
It seemed ok for 4 days, and I installed herald which is a notification addon (hate the fact that mac mail doesn't have any kind of notification of new emails) and guess what the issue has occurred again.
All emails dissappear and the whole mailbox has to re-sync.
I'm getting really frustrated with this and am being forced to consider using Outlook Mac 2011, something Ireally don't want to do.
Does apple actually look at these posts, can someone please help I really don't want to use Outlook