IMAP and Mail 3.5 not importing/moving messages to upper 'INBOX'

Question

Within the last 3 months I finally got an iPhone. This event caused me to change my POP email accounts to IMAP. I have a total of 5 email accounts. They were all POP and are now all IMAP and have been this way for a couple of months.
2 of these accounts are Gmail accounts, one is a dot.mac, and 2 are with an independent web host that does support IMAP.
I have the inbox in the top left with a 'folder' for each account. I then have a list of all my folders I use for local filing. I then have a folder for each IMAP account at the bottom of the list. For the Gmail account there is a nesting of folders. And inside of each folder is typically a 'sent' and 'trash' folder.
The issue I am seeing with new mail coming into my computer is this.
New mail will come into the IMAP folder and SOMETIMES be put in the upper INBOX. There really is no rhyme nor reason as to why the messages do not show up in the top INBOX consistently. It appears to be doing this with all accounts.
One behavior I am able to replicate is this. If I dig into one of the bottom IMAP folders to find an email message that is unread and NOT in the upper INBOX and click on it to read it, THEN go to the upper INBOX the message will now show up as READ.
I can replicate this with every unread email that does not show up in the upper INBOX.
First, why show me the folders at the bottom? If they absolutely need to be there why will they not consistently show or 'move' the unread message into the upper INBOX?
Anyone have insight or suggestions on what I can do to resolve this?
I would like to NOT lose anything I have presently set in mail.
Let me know if you have any questions that can help explaining further.

Answer 1

Oh yes, sorry for the partial answer.
No, I there is no difference whether the emails have an attachment or not, and though a few days ago it seemed to be an on-and-off problem, it seems now that any new email (attachments or no), refuse to hit the INBOX folder.
As far as selections for keeping messages, I do break a bit from the Gmail mailbox behaviors, but only for junk mail, since I rarely use the google web app, and want to confirm junk mail is being labelled properly. All enabling junk mail does for me, basically, is give me a Junk folder in Mail.app that I can point Gmail/Junk to use. Apple Mail rarely picks up its own Junk since Gmail catches it first.
Drafts - stored on server (checked)
Notes - stored on server (checked)
Sent - stored on server (checked - only because I'll click on [Gmail]/sent mail and have it used as the Sent folder.)
Junk - stored on server (never causes copy problems or slowness, Gmail, as i said, catches junk/spam first). Delete after 1 day.
Trash - Move deleted messages to Trash mailbox (checked), Store Deleted messages on Server (checked). Permanently delete after 1 week.