Well in the spirit of fighting ignorance I did finally get an answer to this.
I contacted my DEA file supplier and from the DEA here is the answer.
"A DEA controlled substance registration can begin with one or two alphas. The first letter of a company name, or a person’s last name, is the second character of the DEA number. For example, if the registrant is named “Third Street Pharmacy”, then it will be assign a number such as “FT0123456.” However, if the company’s name begins with a number, for example “3rd Street Pharmacy”, then we insert the number “9” in the second position, that is “F90123456.”
So there you have it. That is what we were seeing in most cases. Some did not start with numbers but they may have registered that way and it was changed later.