It may go up to 3500 RPM because it's trying to cool down the CPU when it becomes hotter, and it's also possible that Speedfan just doesn't work with the HSF. When does it go up the 3500 RPM? Randomly or after playing a game(or something else that requires heavy CPU usage)? You might be able to control the fan speed by going into your BIOS and changing some settings but I'm not entirely sure.
I don't know of any other programs that can increase the fan speed. You can try googling or asking some other members here if they know of one.