I don't have advice, but I can tell you you aren't alone. The shorts did help my daughter, mostly. She almost never does it anymore. But my SON who is NOT wearing a leo is constantly picking at his crotch no matter how many times we tell him not to do it. For him, at least, it must be some strange habit. Not sure. Possibly it is a habit for your daughter, or maybe not. Maybe try a different brand of leo or a different material, if possible?
This reminds me (a bit off topic) but there is one girl on my daughter's team who is really tall and wears a leo that I think is too short for most of the shorter girls. It comes over her hip bones on the sides and sometimes it nearly has the thong effect.... (half of each cheek hanging out). She has to keep fixing it between skills. But you said your daughter's leo isn't too small. I think having a "perfect fit" (as much as possible) might be the best bet for comfort!