Dear Mr./Ms. Still Frustrated:
Dr. Putt is gratified that you have made some improvement and that his previous advice has proven efficacious. He finds your current infrequent malady most interesting. Dr. Putt has had this experience himself, especially in the early morning when conditions are wet. The problem is likely caused by small pieces of grass or dirt on the ball and putter blade that can absorb some of the energy of the stroke or even misdirect the ball. This is more likely to be the case when moisture levels are high so that grass, grains of sand, or dirt stick to the ball and/or putter. It is also more likely on short putts because one is less likely to clean the ball and putter blade on a short putts that are almost tap-ins.
Why don't we take this extra time and effort to clean the ball? We want to complete the short putt as quickly as possible. This lack of golf ball hygiene may be explained in several ways: a sense of etiquette about taking extra time and and minimizing the emotional investment into an endeavor that if successful, will not bring much reward, and if unsuccessful, will reduce our emotional loss.
The ball picked up these confounding materials because it has likely already rolled over the green on the approach putt. The putter face also may have become contaminated on the approach putt. The practice of putting out rather than marking and waiting for those farther away to putt makes this situation more likely.
This problem is the basis of an argument that putts "inside the leather" should be conceded in friendly non-USGA play. However, if one is a frequent tournament player, these putts should almost always be putted out after marking and cleaning, just as one would in a tournament.
If Dr. Putt is on the mark with this observation, then the remedy is obvious. Either don't bother on short putts or treat them with all the seriousness that most professionals do -- practice good golf ball hygiene. If Dr. Putt has misdiagnosed your situation and you are already taking the actions recommended, then you should concentrate on short backswings, acceleration through the ball, and holding the pose at the end of the stroke till the ball comes to rest, hopefully in the bottom of the cup.
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