Ah I see what you mean, but I wasn't thinking you meant it was THAT bad.
To give some context, I don't think I had that issue outside of the first hour or so, where I might want to make a sudden movement, and think in the mindset of an analogue stick, doing a massive movement that flipped me the other way. An example I can think of is the room in portal 2 with the aerial faith plates over the water, where you are forced to make two portals on 2 tiles to keep going, while in the air. I was able to do those, first time, every time I've tried it. Reaching that point was around about 2 hours in I think, because I was messing with the controller a fair bit in certain rooms, like trying to do a 180 turn when entering a lift to the next room, which I now do all the time. I want to say it is your use of mouse acceleration that exacerbates the situation into a mess, but I don't know what you've been doing with the settings outside of that. It could be that the controller is broken for all I know. You should check the support tool to make sure it is 1:1 through out. The edges of mine are not, which is one of the reasons mine is being replaced.