Originally Posted by JoltinJoe
On my MacBook, I use Mail to take in several gmail accounts. They are then sorted into several Smart Mailboxes using rules to organize. The rules work well in OSX Mail, too well maybe. Any email that has been subjected to a rule and sorted into a Smart Mailbox doesn't make it's way to my iPad 3 iOS Mail.
I think you are mistaken somewhere along the lines because Smart Mailboxes don't actually have an effect on the email that is sitting on the mail server or locally. Smart Mailboxes are more like alias on a desktop pc, but with search criteria. They are not "sorted" or moved in anyway and remain in your Inbox or whatever folder they reside in. Smart Mailboxes are basically searching your mail each and every time you select that Smart Mailbox, so again, they are not moved or effected. This is all happening on the fly locally for visual purposes only as it is no different than enter search criteria in the search field, only this allows you to basically remember your search criteria and give it a name for quick access. There is something else going on with your mail and it has nothing to do with Smart Mailboxes.
Perhaps you are creating folders in Apple Mail and have filters in place that are moving them. What this does on Gmail's server is to tag the email with the folder name and if your filters are "moving" the email to that folder, then they are actually tagging them with the folder name and then removing the "Inbox" tag from that email on the Gmail servers. I can't think of any other scenario where by your mail would actually be "moved" if you will (as Gmail doesn't see real folders, only tags and all mail resides in "All Mail")