Unhappy [Q] Will not boot

Please can anyone help me. I have a Galaxy Note 1 (N7000). I recently rooted the phone and at the same time started using an aftermarket 5000mah battery. The phone will boot off the extended battery but will not boot off the standard battery anymore. I use my phone as a GPS when I am on the road and it will not fit in the cradle with the extended battery. I should add that the phone has been upgraded to the latest Android version that was publicly released for the Note and that wiped out the root. It was not booting BEFORE the upgrade and is still not. Can anyone help me please?