Maybe player C likes player A as a DM more than he does with you.
Maybe player A's npc has something more interesting to offer than player B or your NPCs.
Analyze why player A's NPCs are of some interest to player C's PC and build on it. Talking with the players might help you at being more efficient at this.
I, like you, am guilty of this. I have different ways to handling it, some are combinable, but not all.
The main purpose of all of this is to make the game more enjoyable to your players, because the problem with GMPCs is that it tends to ruin the fun for the players. So you have to ask yourself (and/or your players) what specifics are to be avoided. I had groups that enjoyed being the guys that hang around Mr. Coolguy and listen to the story and I had groups that shot him dead.
If the character stays with the group and is important to the story, tell your players directly that you are going to play a PC with them.
So, now my advicelist:
He must be coherent to the rules of the game. He may be twenty levels above the PCs (or whatever concept for power exists) but he still is within game mechanics and thus beatable by game mechanics. If he is injured write that down on his sheet. Don't go over it like 'that scratch wouldn't bother him'.
Make him super-whatever but gamewise unimportant. The one who gives the group their adventure may come over like a young god, yet to the actual story it doesn't matter at all. (The Johnson)
Give him some social problems, small, shy, geeky, clumsy. He actually needs the PCs because he just can't handle the world despite being awesome otherwise.
Handle him like you would have your PC handled by another GM, that makes him more like a character and less like a plot device.
Let him leave the group for prolonged periods and return after that. So there should be multiple sessions without him, then he returns only to leave again after that.
If you want him important to the story let the players try to recruit him into their team (and succeed) rather than forcing them to take someone with them they don't like.
Best Answer
Make the NPCs a vital part of the story.
Earning Trust
Perhaps the NPC is there for the PCs during tough times. Receiving a "get out of jail free card" once in a while from a prominent NPC can go a long way into the PCs caring. Also, increasing the amount of dialogue and feedback between the PCs and the NPCs also go a long way into developing a relationship.
Coercion
Perhaps there is an effect (curse, magic, hostage, blackmail, etc) in place that forces the PC's to care about the NPCs whether they really care to or not. "This or/for that" can be a very good story arc for the PC's to overcome and interact with. If the PC's make a wrong move toward the NPCs, then disaster can strike at any moment.
Overall Effect
The more you have your NPCs as part of the PCs' lives, they will care about them one way or the other. Have drawbacks that affect the PCs or lack of reward if the NPCs are neglected. Have boosts that affect the PCs or abundance of reward if the NPCs are not neglected.
It will really come down to what you, as the storyteller, give the PCs information and facilitation for a relationship with the NPCs. Whenever you read a novel, you as the reader will either care or not care about the protagonist/antagonist due to the writing style of the author. Your NPCs/PCs will be no different. Think of your roleplaying sessions as a chapter in a story novel you are writing. With that frame of mind, the PC's will flourish in ways you haven't seen them perform yet.