Just switched from Lion to Mountain Lion - Now terminal shows up during boot up and when shutting down. How do I stop this?

Just switched from Lion to Mountain Lion - Now, when I start my machine, the terminal shows up and runs through it's thing and then the normal screen shows up. This also happens when I shut down as well - the terminal shows up again. I have a MAC running Mountain Lion at work and this doesn't happen so I'm assuming this is not normal.
While my machine still runs, it's annoying and I fear this will lead to problems if I don't address the situation. How do I ge this to stop? Any help would be greatly appreciated.

They are being sent to the All Mail folder.  The inbox is pretty much unaffected.
I don't want to hide the All Mail folder and forget about it.  I am after the messages gone forever.  Especially from the All Mail folder.
I'm the kind of person who uses email like sms.  I use it to contact people annd delete 95% of the messages after reading.  I don't want them archived.  I don't want them stored in the All Mail folder.  I want them totally gone.
And yes it seems Mail is downloading all my messages over and over.  So my question is how to stop the messages being stored/archived and to instead be totally deleted.
In the gmail settings I found:
Auto-Expunge off - Wait for the client to update the server.
When a message is marked as deleted and expunged from the last visible IMAP folder:  Immediately delete the message forever.  Instead of archiving it like I had set before.  I'm not 100% sure if that'll fix the issue I am having.  I'm sure you'll be able to tell me if I am on the right track.
And thanks for the quick reply.

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