Go to your sound settings and uncheck "Allow applications to take exclusive control of this device" - this option can cause other programs to change the actual sample rate which can cause tuning issues. Make sure your input and output devices are both set to 44,100hz 16-bit as well, that can help.
Thanks. I did that as you suggested, but nothing seems to have changed in terms of the mismatch between the tuning of the computer and the sax.