Thanks Ji for the response.
I have been able to resolve the issue. Please see my other post for the resolution. What I found out was that the code was not assigning any ID to the dynamically added controls and since some of the controls were not generated always, the ID's generated by ASP.NET were also not consistent for same control on Postback. The moment we assigned the "ID' to all the controls, everything started working fine.
The big question before us is why is it working in the older version ASP.NET1.1 and Sharepoint 2003? Can you provide something on this?
Thanks,
Irtaiza