Not sure if this is exactly your issue, but it sounds similar. The only explanation I found is here and it is as follows:
Originally Posted by xXxBRAMBOxXx
There is an Android issue created for it which you can add to here. I'm sure the more folks that post they have it the more attention it will get and you can also get updates that way.
If you have unread messages in your inbox and you delete one, then the unread count changes so it notifies you. It's a bug in the app, been there as long as I can remember on any rom. The notifications go on a change of the unread count, not an increase. If you turn on notify once and leave the gmail notification there then it won't bother you. Also if you star messages instead of leaving them unread then you can keep your unread count at 0