Confused About Engine Evaluations in Closed Positions

     After doing the post on the backward d-Pawn in the Sicilian I played over an annotated game by GM Alex Yermolinsky in which he discussed it and some associated generalities. Curious, I spent considerable time going through the game with Stockfish 6 and Komodo 8 and found that in several cases the engines and Yermolinsky had different opinions. The result was that after letting the engines run for anywhere from 10 to 30 minutes and running a bunch of Shootouts (I have discussed Shootouts before: they allow you to use engines to play out the rest of the game at ever increasing ply depths.), the results didn't always match up with the GM's opinion. Does this mean Yermolinsky was wrong in his positional evaluations? I don't think so because running Shootouts at say 11-15 plies (only about 5-7 or 8 moves) and at seconds per move may not give an accurate result...an engine's forte is tactics, not necessarily positional play. I finally gave up and decided that I would trust the GM's positional judgment. 
     So, the other day I played an interesting 15 minute game on Instant Chess against a fairly decent player (rated mid-1800's) and afterward went over it with Stockfish 6 and Komodo 8. The position was closed with my opponent's pieces all crowded together on the back three ranks and I made a couple of offers of a Pawn; that's the general scenario. The result was similar to the Yermolinsky game in that sometimes the evaluations didn't always match up with the Shootout results; same for my gut feelings. Sometimes my position looked overwhelming and the evaluations confirmed it, but Shootouts showed something unexpected. Another thing that happened is that in a couple of positions the engine's evaluations drastically changed AFTER its recommended move was played. 
     Things like this happen a lot and when they do, it's confusing unless you are rated up around 2600. That's why I always advise believing the GM when it comes to positional evaluations. It's also why experts advise that engines need opening books. The problem is, when analyzing a game like the one I played, there's no 2600 rated GM sitting here with me that can offer any insights when the engine evaluations are not clear.