That's very odd. While backticks will be slower than exec, it shouldn't be that much slower; definitely less than a 1-second difference unless there's a lot of output.

Try tracing the program's execution with strace or truss to see what's happening differently between the two.

It's possible that something in the script is detecting that it's run from the command-line (by noticing that STDIN is a terminal) and doing it's work in the background, or something like that.