All these issues look similar to the ones fixed by Afforess in the Abandon City/Sell Buildings mod.
Basically the popups are not using the default messaging between computers and so need to have it coded into them. I think the fix was done to the events for multiple choice selection but the assumption may be that if there is only one choice then OOS can't happen. Your comment on Great People suggests that this is not the case.
At the moment I know enough to probably identify where the problem is but not enough to fix it.