Dilip,

what you observe might be an indication that your project isn't properly designed and is working unreliable, such unreliable, that it works with the one micro, but quits with a nearly identically working one. This is often observed, for instance, when using a board not containing a solid ground plane, etc. Yes, even a change of cable routing to your board can make your device suddenly stop working properly then.

So, what you observe need not necessarily have to do with the "migration" to the AT89C52 at all, but can demonstrate, that there's something wrong with your basic design. I have seen this in my career many times.

The only escape is to fully analyze the performance of your system by the help of a good scope and many many small test programs. It can mean, that you must redesign the layout, or enhance the filtering or whatsoever.

Good luck,

Kai