...and will allways have grain, colour and texture variations because of this. However, it does sound like your origional floor was a better grade supply of wood, though I wouldn't jump to any conclusions too quickly.
I did once have something like this happen when I bought a couple of new boards for a damaged strip teak floor. The ones I recived were in my oppinion rubish, they had lots of knots and ugly marks in them. It turns out the company thought they were 'rustic' or something like that, and most customers like the old world effect. I informed them I wanted a nice normal floor that didn't look like it was 800 years old. They promptly sent me some good quality boards and everything was fine with them.
If it hasn't be laid down yet there's a good chance of resolving this with them. If it has, try getting a sample of the old board and having that stain mixing done using it. Or, experiment with sample pots, you sometimes can darken or alter the whole effect by using two coats of different stain. Or just another manufacturer's stain might look better. The secrect is to identify the difference and add what it lacks, for example the old looks darker than the new, perhaps two coats of stain on the new floor will give it a closer match? Just experiment with logical tests on spare boards, you'll eventualy get it looking right.