In the past 48 hours it seems that the only way that I can get my Zoho inbox refreshed in mail.app is to manually select "Mailbox/Synchronize". I have tried "Mailbox/Rebuild" but the problem persists. The problem will visually manifest itself when the unread message count disappears in the mailbox pane, and the message headers "disappear" from the inbox. After manually synchronizing they usually reappear (it sometimes takes 2-3 attempts.)
I have no problems accessing my inbox through Zoho's web client. It's always up to date.
I've made no changes to my mail.app IMAP configuration, and no recent updates to my system. I'm running MacOS 10.7.2. Other IMAP mailboxes from non-Zoho services are working fine (Gmail, whatever IMAP server JoyentCloud is running).