My Pfaff dealer told me whenever you are having problem with stitches on the bottom you've threaded the machine wrong. I could have been sewing away for an hour or so without any problem but all of a sudden the stitches are wrong. Go figure. I usually get away with using different threads on the top and bottom but whenever I have a problem I rethread using matching threads it seems to solve the stitch problem.
Anyway, do you have a little brush to clean the bobbin area? You should use it everytime you change the bobbin and anytime you've been sewing for a long time, these are things I've learned through mistakes. My motto is, "If you never make mistakes, how can you ever learn anything?", LOL! May in Jersey