Apple Mail Inbox - messages keep disappearing!

I've been searching and trying various tips from other similar discussions. Here's the deal...I switched from Entourage to Apple Mail about a year ago and imported all of my email folders and messages into Mail. Everything was setup via Gmail POP and I switched to IMAP a few months ago. Realizing that with IMAP I could now move all of my folders from "On My Mac" to "MyName" so that my folders and ALL emails would be visible in Gmail and on my iPhone, I made the move last week. Here's where the issues began.

Each time I moved a folder, everything EXCEPT notes in my Inbox would disappear until the folder was finished moving over. I got used to that and figured it was just Mail being lazy/tired/what have you. I finished moving all of my folders and emails around on Thursday and have STILL been having the Inbox issue. I've tried rebuilding my Inbox, but it only ever seems to work if I select all Mailboxes (Inbox, Drafts, Sent, Trash & Junk) and even then it only works sometimes. I can still see my inbox messages in Gmail and my iPhone, so thankfully they aren't lost.

I have tried repairing permissions, moving library/cache/mail and library/mail/envelope index to my desktop and rebooting. But what do I do after that? I have a feeling it may also be tied to my rules and have deleted both rules plists. Am I supposed to move the folder and files from desktop back to library after rebooting or do I have to reset my entire mail and my 100s of thousands of message??