I used the service at my school and it worked flawlessly.
edited (Just to make sure we're talking about a similar program, my school has LOR sheets that the professors fill out and attach a letter to it and send it to the Pre-Professional office, the office lets you know when letters have arrived and you check off which schools you applied to... then the office sends all the letters at once to the schools). I applied to a LOT of schools and none of them had problems with this method.
Good luck,
Utes