Article usage is idiosyncratic, especially with proper nouns. Popular usage conforms to some extent to the entity's preferred usage— thus, we refer to the Boy Scouts of America but Girl Scouts of the USA; the Gold Star Mothers of America but Blue Star Mothers of America; the Sudan 50 years ago but just Sudan today. No convention is absolute, however. We might think we say the IRS because we would say the Internal Revenue Service, yet we say a professor at UCLA even though the full form would be a professor at the University of California, Los Angeles.
In narrower contexts, insiders may refer to some entity in ways not reflective of how the general public would refer to them, forming part of the jargon. This can be a practical matter; within an organization, she transferred to Sales might be fully understood to mean she transferred to the Sales Department, so the longer form is unnecessary and in fact becomes tedious with repetition. If your office regularly speaks with the OCC, the OTS, the FDIC, and the CFPB, you save a syllable as well as make the names more distinct from one another by dropping the article. Or, maybe you just follow how the boss says it, or something equally mundane. British clothier French Connection's branding as FCUK is said to have originated with the abbreviation for the head office in London used on fax cover sheets.
For what it's worth, in my anecdotal experience working in and around Washington, D.C., dropping the article implies a certain familiarity, of personification. It is as if you were nicknaming an intimate as opposed to simply identifying an entity. I would liken the difference between the FTC needs to rule on this and FTC needs to rule on this to that between My grandmother says so and Grandmother says so. You might use this deliberately to serve as a social signal or group marker, even if on a day-to-day basis, you code switch between work and home without even thinking about it. I have not been able to find a scholarly article on the topic, however.
The use of in hospital, et al has been covered in several past questions, but I think it is a separate phenomenon.