I don't think Farrell is baffled. I do think he is going to force Lester to attack the strike zone next time out and let the cards fall where they may. If Lester is tentative about that or just does not do it, then Farrell and Nieves may well be looking at a different set of issues. However based on what Lester has said (feel great, as in no physical issues) and based on what Nieves and Farrell have said (Lester cannot let hitters dictate whether or not he is going to attack the strike zone) Plan A appears to be attack the strike zone and see what happens.
i don't think they see a specific mechanical flaw for Lester to work on which I can understand. Lester did not appear to do the same thing twice, good or bad last time out and being inconsistent is not a mechanical flaw.
We have seen Lester fall into these blue funks before and that may be all that is going on here. Does not mean it will solve itself overnight but it might. Then again, it might not. Pitcher's complicated animals and Lester is on the complicated end of the pitcher spectrum.