Easiest way is just flashing it separately, you should be able to find the file in Intratech's stock ROM thread.
Never had that happen to me but then again I don't use 3rd party batteries. Specifically due to incompatibilities like this.
Try this, take the battery out for some time then put the original Samsung battery back in and plug the phone into charger. Do the charging while its off and see if it does it properly.
Communicated using an SGS2 droid with XDA premium neurotransmitter while DJ'ing on the Death Star.
As you may be aware of my plight with the phone going dead on me when changing the battery. Well after charging the battery that I had used when carrying out the configuration in a separate charger, I replaced this battery in the phone and it started working. This means that this configuration is carried out on the battery and by changing the battery this configuration will not be compatible. Unfortunately I do need to change the battery at least once in a day due to the intensive use of the phone and some of the apps. like Golf shot when playing golf. Hence I need to go back to the default configuration and abandon your configurations. Can you please guide me how to get the original configuration back. I was thinking of upgrading the kernel to Siyah V2.6.8 and hoping that this might wipe out and the default config will be restored. I will wait for your reply in case I create a bigger blunder. Many thanks.