Maybe it's just because *I* have never had a use for it, but the auto-scroll seems to be more of a burden than anything else. I'm serious...if it was taken out all-together I wouldn't miss it in the slightest. Mind you, that is for my own personal use and experience, so what it would be like for others is debatable. Also, if you could, at least turn the auto-scrolling speed down, and I mean by a lot. In half a second I'm halfway on the other side of the page. Personally I think more customization, and not less, would be of help here, but then again, I'm not bias-free, so you might want to take what I'm saying with a grain of salt.
Hmm...I've heard of some plugins for Paint.net. Maybe to meet half-way, you could make a plugin for Paint.net? This way it is enabled by default in the vanilla software, but with the plugin, it gives the ability to fine tune auto-scroll (example: scroll 10 twips in a given direction), or better yet, to disable it all-together. Odds are that if someone were using this plugin they would know about what is going on from the outset, and if the worse were to happen where they disabled the auto-scroll, the problem could be fixed by either going back to the plugin, or perhaps by removing the plugin, or deleting a config file. I, personally, am used to Firefox, and now Chrome, so I'm well used to having to install plugins (and grease monkey scripts) to get the functionality I prefer. Maybe by making things modular it would work better since the end user would have the customization and control they need.
EDIT:
Good news: for the last few days I had Fluid mouse input unchecked, and in that time, I haven't had a single issue with streaks going halfway across the page. As a test i toggled it back on, and yes, they came back almost immediately. Since I'm using a stylus with my drawing monitor (as apposed to what?) I think there may be a compatibility issue going on here that requires that option to be toggled off.