A similar thing happens to a friend of mine, but only in his Cutter. It started about 6 months or so ago and happens both in space and when taking off from planets (but more often around planets) and starting from normal space. He can be perfectly aligned with the centre of the target, whether that's a planet in the system, another system or the blue escape target. Once the drive is charged up and he's at full throttle, perfectly aligned, it will keep repeating 'align with trajectory' over and over. The only way we've found to trigger the SC/Jump is to repeatedly hit boost.
The fact that it only affects one specific ship of his suggests it's linked to one of the ship's stats or components i.e. speed, mass, power output, thruster type, etc. but no amount of swapping components, upgrading, downgrading, un-engineering or re-engineering has managed to fix it.