I agree, you would think they'd have everything uniform by now - it's been a few weeks already since they unveiled it on the news side.
But I have noticed that things at FOX61 usually move a little slower. I don't think it's their fault, they've always been a small organization, and probably don't have the technical staff to do the things we expect of other stations in this market (3, 8, and 30). Although this will probably change seeing all the staff they're adding and other changes taking place there.
I would imagine (and hope) that they use the new logo uniformally by the time they debut their new Fall lineup next month. They already have the new logo on their mics and other apparel, so I assume we'll see the new logo everywhere at some point.