I sometimes used to run into a problem with SF 6 trying to save a file at 'default' settings rather than the settings of the project. For example, I transfer from a 16/48 DAT recording with SF properly set to record; but when I go to save the recording, it uses the "Default Template" (which is 16/44.1). I had it happen a couple times to me.
Otherwise, I would suspect a sound card setting needs to be changed. I know on my Delta Dio 2496, there is a separate control panel that has to be set to the proper sample rate as well.