Well perl's exec() function as far as I know does nothing more than call the sytem's exec(). update: but yes, I meant the underlying mechanics, not perl's buildin functions.

Running the program manually takes effectively zero seconds, as indicated by my mentions of the fact that running it with exec() is essentially instantaneous.

I thought you meant it started immediately, I didn't see anything about it also finishing quickly.

It may be that the command is checking slowed down / confused by the capturing of it's STDOUT. it might be looking for a tty or something similar. In that case, the easiest solution should be to use system() (or exec(), ofcourse)