No-where does it mention amount of cities or anything else in the rules that I can see that empty cities affect the ER rate.
If I am missing something here please let me know. The city design states 228 jobs, which lines up with the rules, but the planetary stats for ER state 243 jobs. Now I am unsure where the discrepancy lies, but those 15 jobs do not exist anywhere.
Could having an excessive amount of one particular facility cause the ER to stuffup? (It is known that having too many of a particular facility will ruin income stats somehow)
I can only imagine that there is some discrepancy between the stats of the facilities in the City Designer and the rules pages. I'd check those. As you say empty cities have no effect and inappropriate number of facilities also does not affect it.
I'd definitely agree that the problem lies in something on another slab that you cannot see. Have you checked to see if there is a hidden city? If there were other empty slabs or no other slabs at all that would not affect the ER at all. So, either there i\IS indeed another city or the city designer/planet code have an error/bug.
I am investigating the problem first hand and will check for hidden cities. If there is none perhaps an admin could shed some light on the possibilities. I dont need to know exact details but if there is hidden things in the code we could all be calculating things slightly wrong.