Do you mean the mouse control during the entire game is problematic or specifically during scrolling in combat?
zarakon says he has a fix for the scrolling speed involving the cpu settings - I've not tried his settings per se, but like you I could get no better behavior from scrolling by altering the cycles when I tried it. So during battle, I just place the cursor using the minimap ... or scroll very carefully. :)
http://www.gog.com/en/forum/master_of_orion_series/moo2_dosbox_config/post5 However, if your mouse control is always off, I'm not sure if that is the same problem or if the above will help you especially since you already the cycle solution. But maybe his value will help.
P.S. Just in case you weren't aware, you can also mark your post as a question needing to be solved when making a post and the post will light up as a different color and give you the option to mark the thread as solved if/when you get an answer by marking said post. You don't have to use [Problem]. :)