and if one is not already in fantastic shape, yes, it will happen.
just as if one is starting out a new (and brutal) workout regime, it's going to be a few weeks before you feel like you don't have a "cold".
new to distance running ? ? = same thing.
Frank is probably right, in it's being bacteria.
i don't know the mechanics of it, but a really good romp + not being in stellar condition = fun and a sore throat.
once you are in decent shape, and you are making enough horsepower to hurt yourself, and beginning to enjoy it, that is when you will be loading your system hard enough to make your throat hurt. it's all good.
it happens reliably enough that i keep a bottle of listerene in the car to deal with it. (helps a great deal to hit it early)
i ordered your e-myth book.