Sounds like a bunch of garbage to me. Even if you don't log out of skype it only eats a few hundred kbytes a day. I doubt it would eat even a 1m sitting idle. For text your number of bytes is not going to be much more than the number of characters you typed. Sure there is some overhead but it is tiny.
Mostly I suspect the ISP or your roommate is not telling the truth. Skype is very hard to even detect. It looks like random ip addresses and random ports. Sure they can see the main connection to the skype site but no traffic runs over that. Even if you would find a active skype connection the traffic is encrypted so you have no way to tell it was really skype it could be any program.