Same problem, killed boss, scene started again. I killed him again, new day started, then after some dialogue I was kicked to boss scene yet again. I think it has something to do with closing dialogue with X button...
I'm working on a sequel, actually. I already made a new space combat engine with much better graphics and effects and 3d ship models :p Btw, any suggestions about where to find nice-looking low poly space ships models would be great...
Well, Cobra hull has a minimum tech level of 9, so you can only find it on stations with 9+ tech rating. But after a while, most stations have big rating anyway. Also, you have better selection of hulls on mining (asteroid-looking) stations. But otherwise, it's just random, and Cobra has a minimum chance of appearing besides other hulls (about 0.1, while others have 0.3-1).
It's not possible to change spawn point. But you can just not die, or reload if you die. And don't forget that you can wait on station while there are too strong enemies around.