ISR missing intervals in android-2.6.29 kernel


I have an interrupt handler routine using gpio which works on linux-2.6.28-omap, but the same does not work with android-2.6.29.

when i debugged, the gpio is driven correctlty, the interrupt handler routine is being called, but the interval is missing and data arrival is not consistent.

my cpu is idle only. no body uses this gpio.

Anybody can help me , actually what i am missing in new kernel, how to trace and debug it.

Thanks and Regards,