I would say it's because of a growth spurt that you had the tolerance of 325mg phe and as the growth spurt stoped your levels did get higher (but this could be totally wrong, since I haven't heard of any other case where the phe tolerance decreased).
Now you said you grow some muscles and you levels are slightly better. This could be because your body needs protein to build muscles and more muscles need more energy and protein than less muscles (that's why the best marathon runners are skinny). So obviously more muscles leads to more phe tolerance.
You should always be aware that phe tolerance is a variable and it can change from time to time, especially if you are sportif.
So better go and see your dietican sometime to check back what amount of phe you're allowed.
And if your tolerance is set to a lower amount now you sadly have to fill your diet with even more lo-pro food.