Finally, something on this forum I'm qualified to answer! Yes, genetic differences in smell are highly possible. As Ray pointed out, there are two obvious genetic differences here: the one in the plant, and the one in your nose!
Broadly, the way smell works is that there are about 400 unique types of neurons (together they are the olfactory sensory neurons) way up in the nose. Each one expresses a protein that causes it to become more active when a certain compound bind to it. Some compounds may bind to multiple olfactory sensory neurons, and some (most) smells are made up of multiple compounds. Likewise, different compounds may bind to the same set of olfactory sensory neurons (rubbing alcohol and vodka smell about the same but are different compounds).
What we perceive as a "smell" is the population code (i.e. on, off, off, on, on, on, on...) for each of the types of neurons. The way a population code leads to a certain odor percept is not currently well understood. That is to say, we know it happens but if you gave someone (or even someone with a state-of-the-art algorithm) a olfactory population code, they could not predict how it is going to smell. This is in contrast to the visual system where we have a very good idea for how light produces codes in the retina that lead to vision.
Now why might you be unable to smell something that others can smell?
Individual differences re very common in the genes that code for the proteins that determine the selectivity (which compounds they bind to) of olfactory sensory neurons. You are probably missing one (or it is slightly mutated so it is selective for something else) that binds to the compound that the plant produces. I am a neuroscientist, not a horticulturist so I can't speak to what happened in the plant's genes to cause it to produce a different odor than the other one but it seems like just another result of sexual reproduction.
By the way, I totally understand how this feels. Roses have no scent to me. It really seems limited to roses, I can smell every other flower as well as anyone else including beach roses. But classic roses, rose water and rose perfume I cannot smell. Or if I can, I am getting the other scents of them (like vegetal, sharp, soapy ones).