sudheer_nm,

Let me see if I'm reading this right....
You have an active database and you have some sort of make shift standby database created using perl scripts? The copy commands that you are using to get the datafiles across sound like to be the problem.

If this is the case, why don't you just set up an actual Oracle standby database? Sounds to me that would be the way to go (You know, less moving parts the better). Besides, if you're running 9i the features that you could use for your standby are awesome.