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Problem in setting duration between the pulses using interrupt

Hi all,

I'm getting a set of variable frequency, and when I set the duration for
the different time like 1hr,2hr etc the frequency and time runs and stops,
for the given time.
But the frequency for any duration of time set it runs faster and reaches
final frequency and stops[like initially 5hz,6,7,8,9,10hz stops].
I'm using timer1 registers for timer interrupt, and timer0 registers for pwm variation in
LPC2148.How to set the duration between the pulses in interrupt?