Hi - Don't know if this will help or not, but thought I'd give it 1 more shot and provide some follow up information.
Per your suggestion, I've tried every shader in the settings list. No luck. This seems to happen randomly after a gunfight, or looting. Here's just 1 example.
Mission 26: Crossfire Chapter 6 - Brennigan's Coordinates. I came across the first ship you had to loot. I fired at it and hit "B" to loot. As soon as I tractored in the loot,
it locked up. I was able to click on the waypoint but had to use F2 key to "Go To". The whole trip to the waypoint I had to manually keep pointing the ship toward the waypoint. I then had to use "F3" to Dock. The animation moves through the portal fine, but when I reach the other side, still locked. There are several jumps in this mission and I had to do the same until I got to a station and docked. When I launch to space after going through the cut scene, everything is fine again until another battle or tractor. I don't remember what mission it was, but this all started on a previous mission where you had to go to a dig site on a planet. When leaving the planet, you have to fight off some Corsair's in the atmosphere and then return to the dig site. I basically had to limp back to the dig site. Once I docked, went through the cut scene and launched it was fixed again.
I know it's not my Logitech G903 Lightspeed mouse, because it works fine in Vanilla Freelancer, and all my other games. I am running a Core I7 8700K processor, Geforce RTX 2070Ultra XC Video Card, 64GB Corsair Vengeance PRO Ram, on a Gigabyte Aorus Z390 Ultra Motherboard.
Again, I appreciate your time and patience. If there isn't a solution, I understand but thought this information might be useful.
Thank You