I'm stuck here having exactly the same problem. The funny thing is, it all started since that Mail for Mavericks update, 1.0 which I installed yesterday, which irronically stated it should solve some instability problems (that I was not experincing at all) and made things go completely wrong. I tried to delete and add the account again, and it is not making things better. The weird thing is that I can see the content of some folders, such as deleted items, and inconsistent as it is, it might not display it anymore after I try to go back to this folder. For example, I thought I solved the problem this afternoon, after I had deleted the account and added it for the third time, and let my computer sit there for a while and sync. When I returned to my Mac after an hour, I was under the impression that it synced my inbox correctly, but then when I clicked on another folder to see what's inside and got back to inbox afterwards, it was completely empty again. Mail is just very unstable and the problems are increddibly inconsistent. I think I am now going to try to add the account manually. I will let you know what happens.