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Maybe double check your test kit? Are you the only one who can feed the tank? How has skimmer performance been during this issue?
I haven't noticed you mention other signs of nutrient issues - any excess algae growth or other indications of your nitrate issue?
I'm not sure I understand why you have the pellet reactor on a new 100 gallon system with just a few small fish in it anyway. I'd shut it down completely until A) you need it and B) you get this situation figured out.
As you have alluded yourself: there's no good reason to have nutrient issues on a new, reasonably-stocked, not-overfed tank like this.
The reactor isn't going to help with whatever is causing your issue IMO.
-Matt

