Jango kept Kuro's flag cause he was told to, I think… Kuro still referred to the Kuro Neko as his Pirate Crew, even after Jango was running them.
Personally, I still am under the impression Do Flamingo is Luffy's Grandfather. Why? It's simple:
1. Doflamingo: That means he could be a D. Since all the Schibukai have an animal nickname, that could be his middle name. Donquixote D. Oflamingo could be his real name.
2. He's someone that even Kuzan would have a helluva time fighting.
3. He takes an interest in Luffy, and decides to persue him. Maybe he wanted to see if his Grandson had what it took to be a Grand Line Pirate Captain.
4. His whole spiel about the New Age and the Elite Pirates being the only survivors could be something he ingrained into Luffy and Ace when they were children. That could be part of Luffy's fear toward him... if DoFlamingo's dream became a reality, many people would be screwed, something that Luffy doesn't want.
5. He's something that Luffy could fear anyway. The power to play people like marionettes? That's a very dangerous power.
6. His disrespect for the Marines paralells along with Luffy's. It isn't a blatant "I'm killing the marines" type of deal, it's like Luffy's: "If you're in my way, I'll kick my ass. I could care less what you think of me, just don't stop me from my goals." That would explain the disrespect he showed Sengoku and Crane at the meeting.