I've noticed three major bugs on my system:
-Specular lighting doesn't work at all. I just get standard lighting. 3.5.5 does not have this problem.
-I can't jump out. Whenever I try, I get a message at the top of the screen reading "Engine failure. Cannot engage warp drive." This does not happen in 3.5.5.
-Sometimes the blue lines that some other members mentioned appear around certain menu items. The menu doesn't do this in 3.5.5.
Also, can you give the person installing 3.6 a choice between the new "hybrid" thrusters and Lightspeed's old ones. I really dislike the new ones and I love the old ones. They looked far more powerful and the Shivan thrusters actually looked like some kind of engine plume (just by looking at the original FS2 Shivan thruster graphics, it's obvious that they wanted them to be much like the other species engine plumes only, well, red.