Yeah, playing 3 notes per string scales is one of the most difficult things a guitarist can do, IMHO. It’s hard to translate your fast right hand motion to scalar runs right away.
Can you give any more description of the motion you’re using? Is it elbow, wrist, forearm? Also, is it USX or DSX? A video would obviously be best!
Depending on what you’re using, I’d recommend just working on playing to the strength of the primary motion - so, if you’re using USX, try using your fast picking to play even numbers of notes per string (like Yngwie-style licks). You can even try 3nps scales, but just play each 3rd note two times, giving you 4 notes per string. Does that feel comfortable?
After you feel like you’ve got that down, trying odd-numbered groupings would be something to look into. Most players have to use their primary motion along with a secondary motion (like Vinnie Moore’s forearm rotation) to help with unusual string changes, so that secondary motion might be the next step in your development, after you get more comfortable with your standard escape angle.
EDIT - It sounds like you might be using a DSX motion, so try playing fast lines that only end on downstrokes. For instance, try playing:
If you’re using DSX, that should feel fairly comfortable, because all the string changes are after downstrokes.
