Mailbox creating multiple entries of the same mail

I have my gmail account setup with Mail. I have several labels with filters in my gmail account. Let's say my gmail has 5000 mails when browsed through the browser and using only 5GB of Gmail space, my IMAP mailbox when clicked on All mail shows 16000 mails including the ones within the labels and taking 12GB of my harddrive... Is there a way i can avoid this duplication and act just like my gmail does??? If I have an attchment, it's reflecting once in my inbox, once in my label and once in all mail... though I delete in one place it's still there in other.... taking up all the space.

I'm sure lot of people are facing this issue.... It'll be great if someone can help me solve this weird issue.

Appreciate it.

FYI: I was using Snowleapard and just migrated to Lion. I have the same problem in Snowleapard too.