while we're at it (sorry for threadjacking): since when does development mandate only have 1 level? was quite surprised the other day, though I think it's a good change, since the two levels really were quite powerful indeed.
@ topic: don't beat yourself up about it. some boni are really just strange, like the xtra well together with the minus well size and the like. it may just be one of those combinations that end up being pointless. though penal colonies does have another effect, no? like faster structure build rates. if yes, then be happy you can enjoy the pros without suffering the cons.