Mhh, i noticed another thing which is possbly related to this.
The reset button in a script config dialog, does not reset the config item to what is the current default in the script. It does reset to some defaults used anytime before, but if the script-defaults were changed for a config item, the reset button does not reset to that new default. I'd need to remove/readd or rename the config item in the script, to get the reset button to reset to the actual defaults. DO seems to remember the defaults "too long" it seems.
This adds to my impression, that there is some sync-problem at times between DO, script defaults and settings in use. I'm afraid I cannot provide any more details currently, surely will if I really get behind what's going on, but maybe this detail is a another piece for the puzzle.