Problems with gmail imap and not seeing new messages in inbox

I have done countless searches and have not been able to find anything that works. I am gathering that mail on the iPhone 4 and the ipad is not illy compatible. Here is what I am having trouble with:
I recently switched my gmail from pop to imap. The reason behind this is that I could not have mail running on my MacBook and still see my messages on my iPhone 4 or ipad at the same time. What would happen is that any new messages would download onto my MacBook and I could not see them in mail in the inbox on my iPhone and ipad. So, I switched to imap so that I could leave mail running on all my devices and be able to see the same messages no matter what I was viewing them with. Here is the next problem. Now for some reason, only some messages go to the inbox, all of the rest go to the"all mail" folder. Is there a way to fix this so that I can view all of my messages in the "all inboxes" in mail?
Maybe I am misunderstanding how this is supposed to work but any help is appreciated. I have checked the filter settings in gmail (which I had none) and the labels and still nothing works. I have also verified from the gmail help my mail and gmail settings.
Hopefully this makes sense. Thanks for the help!

No ideas?

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1. Go to Apple Menu > System Preferences > Accounts and create a new user account for testing purposes.
2. Either log out of your main user account or just quit Mail so that it does not interfere with the other user account.
3. Log in as the newly created user and set up the Gmail IMAP account there.
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<hr>
Do you have any Mail plug-ins or system utilities that could interfere with Mail? In the Finder, go to each of the following folders (if they exist). What do you see there?
/Library/StartupItems/
/Library/LaunchDaemons/
/Library/LaunchAgents/
/Library/InputManagers/
/Library/Mail/Bundles/
~/Library/LaunchAgents/
~/Library/InputManagers/
~/Library/Mail/Bundles/
To make accurately reporting this information easier, you may open /Applications/Utilities/Terminal, type the following command (you can just copy it here and paste it in Terminal), and press <Return>. You can then copy the output of that command from Terminal and paste it in your reply to this post:
ls -1 /Library/StartupItems /Library/LaunchDaemons /Library/LaunchAgents /Library/InputManagers /Library/Mail/Bundles ~/Library/LaunchAgents ~/Library/InputManagers ~/Library/Mail/Bundles
Note: For those not familiarized with the ~/ notation, it refers to the user’s home folder. You can easily locate any of the folders referred to in this post by copying the folder path here, doing Go > Go to Folder in the Finder, and pasting the folder path there.

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http://help.yahoo.com/l/us/yahoo/mobile/comms/mail/imap-01.html
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http://mail.google.com/support/bin/answer.py?answer=78799
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