Google mail doesn't push this info about read email like mobile me for example.
I have to click through my email on my ipad, iPhone and MacBook for google mail.
That is one thing I have always wanted with iPhone os. Mark as read button.
Looks like it was caused by my Hotmail account which is linked to my Gmail, leaving 11000 unread messages in Gmail.
I setup my gmail in Outlook, downloaded all the headers (still took over an hour!), then marked all as read and synched with the Imap folder.
Then I removed the Gmail account from my iPad and re-set it up. Strangely, the iPad remembered previous settings and still said I had unread mail, so I removed it again, did a hard reset and set it up yet again.