Ok, I just found a rather curious bug? here...

To simulate a guided missile first coming off the rail of a fighter, and then igniting a moment later, I was doing this:
Stage 1: Homing Seeker, Speed 100, Inacuracy -90, Sub to stage 2 after a moment
Stage 2: Normal homing missile, Speed 500

This didn't work out quite right. It looks good if you are stationary, but lookes funny depending of the speed and direction of the fighter. This is because the missile comes off the rail at 100 speed sideways relative to the background, NOT relative to your fighter. So this missile is not moving forward at all.

So I abandoned the idea, and used this:
Stage 1: Homing Seeker, Speed 250, Inacuracy 10, Sub to stage 2 after a moment
Stage 2: Normal homing missile, Speed 500

This looks decent enough, since the 250 speed is slightly faster than the fighters, yet you can still see visible acceleration when the motor ignites.
It looks a little bit funny if the fighter happens to be going backwards, but it's not too bad.

Then, noticing something about unguided projectiles, I came back to the problem and tried this:
Stage 1: Unguided , Speed 50, Inacuracy -90, Sub to stage 2 after a moment
Stage 2: Normal homing missile, Speed 500

This worked perfectly! The unguided projectile's velocity is relative to the launching ship, so the missile does indeed appear to float off the rail, then boost in the direction it's facing. And even though it launches as an unguided projectile, if you have a target, it will still home in on it when it subs.

The problem I encountered was that suddenly my AI fighters were behaving strangely.
They would some times launch missiles in the wrong direction, and then sputter around and begin spinning or ocillating in place.

So I put the missile characterstics back, and without changing anything else, suddenly the AI is behaving normally again.

Apparently, the weapon was consfusing the AI somehow, but I haven't the faintest idea why.

Bizarre. Actually, it would be more realistic if it's barely moving. Stick with 250+guided and that'll solve the problem.

Oh man, I wanna make Hellhounds do that. It would look so cool and be really easy to do.

I'm not sure why your fighters starting acting funny when you changed the guidance type to "unguided", but the negative inaccuracy working/not-quite-working is perfectly normal. Guided weapons always have speed relative to the system background, while unguided projectiles have speed relative to the firing ship. Rockets are odd, in that they fire with the velocity of the firing ship, but then accelerate (or decelerate) to a speed relative to the system background. Beams, of course, don't count, and fighters, I believe, are launched with a velocity relative to the firing ship.

You may want to try using front quadrant or rocket guidance for the first stage, to see if they affect the AI in the same way that normal unguided weapons do.

Edwards