Because Garibaldi had already quit, Ivanova was gone, and Sheridan went political, the only ones left in the black AoL uniforms were Zack and Dr. Franklin. After Dr. Franklin left for Earth, he probably wore no uniform at all, leaving only Zack, and with him being picky about clothes, who knows what he decided to wear after that.
I've noticed the same thing, however, about Corwin and the other C&C officers. The always wear a standard grey shirt, but it doesn't even look like a uniform. It's more like the equivalent of today's business casual, except that the shirts did all look the same. Security also never goes back to the grey uniforms; they continue to wear the olive, slightly more GROPO-looking outfits with the padded black shoulders.
It does make me wonder... When B5 broke away from Earth, how many people actually resigned from Earth Force? Was it really everybody? Or, was their Earth Force status more "on hold" (if that's even possible) until the conflict was over? If so, you'd think they would have gone back to the blue command uniforms and grey secutiry uniforms after the civil war was over.
Is it possible to be in a military organization but wear a different uniform--or no uniform at all--due to the unique aspects of your post? Is that the reason the uniforms were different in Crusade, or was the Excalibur more of an Alliance ship rather than an Earth Force ship?