It's possible that the male is maturing and the naturual order will be to have the female step back a bit. I'm betting she'll come around once he gets thru his "teenage" years :-D
We had a death of the youngest female barn cat this summer, she was pregnant. The other three - 2 males (one, her sire) and the female mother - were obviously affected by the status quo change, and for nearly 3 weeks were generally ignoring of each other. It was so obvious they were grieving, as we all were. Then slowly things got back to normal and they all ate from the same dish each night, palled around together, took naps near each other. Now the season has changed and the non-sire male is on the outs with the other two who are more dominant at feeding time. I'm betting it'll pass.
Jan in VA