It sounds like there might be something wrong with the second lot itself, although I don't know why it's being so persistent. It's very unusual for there not to be an NRaas menu on any lot that isn't totally vacant if you have MasterController in play, and an MC Reset of the lot is what I would want to suggest. In addition to the above, if the lot were being recognized as a school you should also be seeing Join the Education Career (if you have Ambitions) and Take a Painting Class.
Have you let the game clock run for a bit after placing the second school? If you save the game (or rather save as), quit all the way to the desktop, then reload, does the menu then appear? Also, possibly only the school map tag is showing up for you rather than the lot tag, does it matter if you click on the ground of the lot or a wall of the building instead of the map tag?
Generally speaking though, support questions about NRaas mods are better asked at NRaas. It's kind of what we are there for. :)