[Suicide Junkie]

That would happen when you are just barely able to intercept it.

One thing to note is that if you try to burn at 100% power up to halfway, and then decelerate at 100% power the rest of the way... then you have NO ACCEL left over to correct for rounding errors.

You should probably have the ship try to use 90% of its maximum accel, and try more thrust if that isn't enough...
If both ships are of equal accel, you've got to just head for it and hope the target isn't actively trying to avoid you.