Dear matburt, anoek and community!
Today I almost had a won game miscounted as a loss. Fortunately, my lead was big enough to catch the error.
The difference in points stems from the fact that there were some stones of mine, which were perfectly alive and connected to my groups using a bamboo joint and a kosumi shape, that had been automatically marked ‘dead’. Both players then neglected to switch them to live status.
In my case, that was because I have always assumed that such stones would not be counted as prisoners unless they were also placed in enemy territory (with a white square over them).
You may wonder how in the world I never noticed that before, especially considering that I have been playing on this server since before the name change! Even in this game, I was alerted to the discrepancy by someone else.
True, it doesn’t speak well for my counting abilities.
However, the scoring mechanism also does its part to be confusing.
First of all, there is absolutely no reason to assume that any stone could ever be counted as prisoner if it was not captured or left inside enemy territory (i.e. the area where the opponent makes their points). This is according to the Japanese Rules and, presumably, all other rulesets of Go. The opposite would be very counter-intuitive to me.
Second, the way the stones are displayed (half-transparent) does not clearly indicate that they are prisoners. They are merely strings of stones that are not adjacent to friendly territory. It gives the appearance as though the auto detection cannot determine their status for this reason and leaves them in some half-state. That would be fine as they have no bearing on territory anyway.
Finally, these kind of neutral stones are really not hard to count. For hard groups in enemy territory and seki, where the life-and-death depends on theoretically possible moves, the status may have to be determined by a human. Stones which are placed next to neutral points are trivial to auto-count by comparison - they are obviously all alive unless explicitly marked dead! If auto-score does anything at all, it should first leave such stones well alone.
My feature suggestion is that stones outside any territory should always in all circumstances be presumed alive in auto-scoring.
Edit: As it turns out, stones occassionally get auto-marked dead even in friendly territory. This is just as wrong and should also be changed.