The fare is priced in Euro but stored in NUC, which is "neutral unit of conversion" (but where 1 USD = 1 NUC, so I don't understand the point). So, it's possible that even though the price didn't change, the underlying fare (measured in NUC) did, and so therefore they're detecting a fare difference.

If that's the case, even though you already flew part of the journey, the whole ticket (including the part you flew) is being re-converted from NUC, and thus the exchange rate difference applies to the whole trip.

I'm still making a few guesses here, but I think that's what's happening.

At least you were able to get it waived, though.