I'm guessing that the toilet that now makes the strange sound is not serviced by the new cutoff valves. Is it possible that when you shut off your water supply to do the laundry cutoffs, that you dislodged some junk that has now traveled to your toilet fill valve?
While I love ball valves to pieces, the laundry is probably the one place I would not use them. This is because these valves are your only means to regulate the mixture going into the washer. I always find it takes some tweaking to get the temperature right and ball valves don't have the degree of control you need.