It's impossible for anyone to help you, for the simple reason that you're not giving your nonworking code. The following should help you post an answerable question. It might even let you ask more precisely, or find the problem yourself!

Try to write a short while loop which "calls a perl script using backticks". Does it work? Is it executed just once, or several times? If it's executed just the one time, try replacing the perl script call with a print statement. Does that execute just once? Is your loop executing more than once?

Try to find short, nonworking code, and post that. Then we might be able to help you.