How do I find the leaks in my game?

[CaptainNurple]

So I realize this question is going to be rather broad, but hopefully you guys will be able to offer me a bit of useful advice.

So I've logged about 3,000 hands on the PP $.5/$1 tables, and I feel like I'm playing pretty well, but I just don't seem to be playing profitably overall.

According to PTO I've got a VPIP of 20%, and a PF Raise of 2.3%, but only a 28% "Won $ WSF", a 39% "Went to SD", and a 61% "Won $ at SD". These stats include the week or so I was learning the game, so they might be slightly skewed downward, but it still looks statistically like there's something seriously wrong with my game, because I'm running at -$1.33 BB/100, even though I feel like I'm closely following starting hand selection, building big pots early, and trying to be sure to fold non-nut (draw) hands and focusing as much as possible on playing for the scoop.

I guess my question is how I can use whatever tools are available to figure out the problem with my game. I was browsing through hands on PTO and it looks like a lot of my net losses come from very strong hands that just weren't the nuts (either from getting out-drawn, or just from being straight up beaten by the nuts).

I can go into more detail if necessary, but I'm hoping people might have some advice for what I can do to pull my play up into the solidly winning realm. My bankroll has been hovering for 2 or 3 weeks now (I seem to play better somehow when it drops down and thus regain my losses...), and I'd like to see it start moving upward.