Getting millisecond accuracy is pretty tricky business, and you might be better off with a professional package designed for this kind of thing. I work in a linguistics lab (phonetics), and we use E-Prime from pstnet.com. It's designed for use with Windows.

Even if you don't want to use E-Prime, their documentation has some nice discussion of the kinds of technical problems you need to address in a Windows environment for getting millisecond accuracy. Maybe Time::HiRes addresses all these problems already.