So the raid system is based off of your base score (which is the house icon at the left) so this shouldn't affect the system. Their are several 'types' of missions for building. One is HAVE X number of things built and BUILD X number of new things. It is definitely cheesing the system; I use it when I retest all the missions :)
I'll look into the resetting data buttons. Maybe I messed them up some how.
I remember now I disabled rotation for the work stations because of the way the items spawned or maybe the UI display? I was probably just being lazy while doing other things and not wanting to recalculate the positions of everything lol