Unless I am mistaken, FIP assumes a league average LOB%, attempting to remove luck from the equation. This makes sense, but I'm afraid adjusting for the league average doesn't solve this problem.
Surely, pitchers who record more outs than the average pitcher will also record more outs than the average pitcher with men on base. This may explain part of the large disparity between FIP and ERA in a given player.
I want to be clear that I'm not making the argument that good pitchers are better at holding runners on base. I'm not arguing that, because holding runners on base has shown to be non-repeatable.
Above average pitchers should be above average with men on base, and below average pitchers should be below average with men on base.
The solution, I presume, would be calculating a pitcher's expected LOB%, and incorporating that into the FIP formula. If a pitcher's LOB% is higher or lower than expected, their FIP should reflect this.
I feel like I must be missing something, because this seems very obvious, and the Fangraphs staff is much more knowledgeable on advanced metrics then myself. Edit: Why no answers? Is this Q and A page updated at all?