I think you have 2 issues: 1) as mentioned above it was done at a separate time and 2) the other floor didn't age the same as it was covered. We had this same issue with some vinyl and carpet in house where the wood was covered for 60 yrs. It had one of those swervy metal things and after the floor was redone, you could see the distinction. And, it was nobody's fault, it's just that the light penetrated it differently.
(In our case, we woven in some new hardwood and refinished again to avoid a noticeable line).
And, yes, it sounds like they used the wrong finish. Usually, it's only the top coat that matters. And, when they add another coat (assuming they are screening), it take off 1/2 to 3/4 of the layer under...so I wouldn't worry to much about adding another coat. I never would have done 25% glossy, but now that it's done, you need to decide what to do going forward.
It will never come out the same as the other given the # of coats, types of poly and the underlying issue that it was covered. So you need to come to grips with that and determine which is the lesser of 2 evils. You could try another coat of semi (assuming that's what was used on the other area) or try a complete redo.
Debbie Gartner, aka The Flooring Girl
http://TheFlooringGirl.comWestchester County, NY