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I usually scan LED displays at several hundred Hertz. I find 100 Hz distracting, because I see the flicker when I slightly move the LED or my eyes, especially if the LED is located in my eye's peripheral field.
Thanks all....that was what I suspected!! Actually I'm using timer0 overflow interrupt at 32mSec for multiplexing and for other purpose as well!! If I lower down its time period other....timing factor will get disturbed, so how to cope up with this trouble. BTW, I'm using 90S2313.
Although I don't know much about Atmel, but you may want to poll the timer rather than using its interrupt, you can test the vlaue of the timer to see whether it has passed a predefined number, if so, go to display routine.