Based on what I experienced, I think there's something to add:

1) After a time of playing with script activated (wheter I repair or not) my Government buildings get 100% damaged.
2) This only happens with Government buildings either builded or repaired by me, thus only in conquered settlements or settlements that have rioted.
3) This problem is AFAIK not related to quitting a campaign and starting a new one in the same RTW session, as this happens (well, that's what I experienced) irrespective of the number of times the EBBS script is activated.
4) Whenever I switch to a new/other campaign and reactivate the script, nothing special happened.
5) If the faction of which the settlements, in which those Government buildings get damaged, have been taken is destroyed, the time between the first and the second round of damaged Governments seems to increase, so maybe it also has something to do with enemy spies entering the settlements.
6) The experience mentioned above, isn't due to a loss of public order, so any spy involved has very limitted effect. This means, that it's maybe some (flawed) conditional involved, rather than actual in game reality. This conditional is either part of the script, or of the source code.

Of course, I can be a rather strange exception, who knows...