Terribly sorry; really thought I might be able to help. If you find a solution elsewhere, please post it here - I'd like to know what eventually fixes the problem. Good luck.
clocutron
Interesting. I hadn't noticed that. And I guess I had just assumed that you would be playing the Trinity option and didn't think about the base game and first expansion. Of course, it's been a while since I played this and I'm not even sure if I actually finished or not.
Okay, a couple of interesting things I've come across. #1) The more I search for this issue, the more I'm finding evidence of people experiencing it in Sins of a Solar Empire: Rebellion rather than in Trinity. #2) I just reinstalled Trinity and I'm finding the system cursor setting exactly as I described it to you, so I'm not entirely sure where you're looking. I'm going to try to add a screenshot below: <img src="https://cdn.stardock.us/forums/59/65/5965145/ef113702-ac78-48ec-83f2-40
Crap. Now I wonder what game I was thinking of. Sorry to waste your time with that suggestion. I've got some time tonight - I'll see if I can come up with anything else. I swear I had the exact problem you described so hopefully something will jar my memory.
If I remember correctly, you can fix this simply by changing the setting to use a system cursor instead of the fancy game cursor. Go into the game's settings > video > check "Use System Cursor." This will give you a standard Windows cursor in place of the stylized in-game cursor and, hopefully, will fix your stuttering issue. Good luck.