I didn't have that happen, but I have a few bugs as well...Shaundi using the Saints Pallette option, her outfit is all white, on the ship only, in the simulation she appears like your screen shots. And per your Readme instructions that come with version 2.2...Do you simply put the npc_color_palette.xtbl file in the SRIV installation directory as well? You don't mention what should be done for that. (just asking in case it has to go some place else for the ship to see the outfit changes).
The mission "Talkie Talkie"...where you go speak with Matt for 'spreading game play out'. *rolls eyes* Really Volition? Anyways, his Homie comes back as "Unavailable". So it basically prevents you from continuing on in the main quest...since you need to talk to Matt in order to get to the next mission, "The girl who hates the 50's"
Love that you put Johnny back in his street clothing. He just didn't 'look like Johnny'...in that corny space suit. And Ben King...for some odd reason he's appearing on the ship as one of the White House secret service guys. Hair, beard, and in a suit and tie. But that's a bug I can live with. LOL! I kind of like that look on him. (But wanted to report it anyways).
Oh, and just a suggestion...Thought of this after posting my bug report above this.
But I noticed that during the Kinzie Gambit mission and Talkie Talkie one....Kinzie and Keith David are naturally gone from being available. Kinzie being captured by the Zin and Keith off in his own little dream world of becoming President. So it makes sense that their darkened out in your phone contacts. BUT your new added Homies ARE available. At a time like that, I'd suspect that calling them would get buggy???
So my suggestion is to not have them available at this period of time.
*Editing in a few hours later* - OK, I had some nasty issues with this mod tonight. As I mentioned in my post above this one, Matt at one time was showing as 'Unavailable'. This also struck Asha. I began her MI6 missions. (Run the race, stop Zin patrol, protect Virus Injection, shut down Hot spot) When I finished the last part of that series of quests, I was SUPPOSED to meet up with Asha back on the ship. Whenever I'd highlight that portion in my journal, I'd get the "Homie Unavailable" window. She was on the ship and I could talk to her. She'd just never acknowledge the quest being finished. So then I uninstalled your mod. That didn't solve it. I went back in save games prior to starting the quest. That didn't solve it. I had to go back a really good portion, to a save game prior to me installing your mod.
It was really weird. However, I have been having some issues recently. Issues even prior to your mod. So I don't want to alarm anyone against using your mod. I might just be due to issues that I've been having. I don't know. I did just want to make you aware of it though. I'm kind of disappointed too. I wanted Asha's White House model. I just like it a lot better.