Technically, there are three things to look at.
Who is responsible for the Ytsejam creative output? That was always Mike Portnoy who assembled the releases, decided what to release, etc. He has not been involved since he left the band and no new releases have happened (with the exception of the Happy Holidays free download which was sort of a Ytsejam release that the current band was responsible for).
John Petrucci has always, and to this day, is responsible for the business side of Ytsejam, such as making sure products are stocked and I think he was the person that got the releases produced onto CD, etc.
A guy named Mike Brown fulfills the orders and coincidentally I think is also Mike Portnoy's webmaster. This is a side job for him which would explain why communication hasn't always been great, orders take a while to fulfill, etc.