One guess is you're undervaluing defense relative to this other stuff. Hamilton has the 2nd best Def average in the league, so it'd be real tough for me to predict them to go 0-16. Similar for RPI. We rate really poorly in LP, but have by far the best team Def in the league. I think your formula is probably underestimating the value of that.
Hammy has 20 points in Def on StL, and I think that should definitely outweigh a similar amount of LP or Per. When you consider that your LP/Per is only measuring a few players, while Def is the entire team, you almost have to count Def more. 20 points in "top two LP" is basically 40 more skill points. 20 points in team Def is more like 200, depending on the number of players.
My suggestion would be to try playing with the weights on these variables. I'd also think about including team Ath, since I think that might be the #1 rating that correlates to success right now. Or maybe a combined Ath/Spd/Def variable. Thanks for posting this btw, interesting stuff!