I have the same kind of problem. However, it's just a little different. I'm sure someone with gobs of plumbing experience can tell me exactly what to do to fix it.

Home: 2 Full Bathrooms, built on a slab, no water softener, city water, home is 9 years old

Problem: Flush the toilet. It goes through almost all the filling process. It is almost filled when a fog horn sound is heard (not especially from the toilet itself) which is heard throughout the entire house...and it is LOUD. When the toilet is finished filling, it stops. Do it again, same thing. And did I mention it is LOUD and it echoes through the whole house? More noise from the rest of the house than right next to the toilet. But IT IS associated with the toilet filling.

I have checked all valves and toilet "guts". Everything seems to be just as good as the day it was purchased.