There could be a number of reasons why this is happening depending on your computer system, your method for PTT and the settings you've chosen for rendering and playing back.
I'll relate what happens on my system with more advanced audio hardware/software/and external video sync equipment installed and how I get around this problem.
My audio hardware and software does not "autoswitch" to the sampling rate of the media file being output, it must be set manually to agree with the file.
This is further complicated by the fact that Video Factory previews all files from the timeline at 44.1k, converting the 48k video audio files on the fly to seamlessly preview them in conjuction with music files from CD. At least that's my guess on why it's done that way. At any rate, I have to manually set my audio hardware to 44.1k for previewing from VF, and then manually set it to 48k when I use or output the rendered file.
VF automatically reverses the sampling rate conversion when the file is rendered. The 48k video clip audio is left as is, and the 44.1k CD audio files are upconverted during rendering so that the final file is all 48k for output back to dv tape. My guess is that your audio hardware and software are locked at 44.1k. Previewing from VF is therefore fine, but when you use the final rendered file you need to manually set to 48k audio sampling rate.
Again, there could be several other activities and settings that could be causing this problem, but that's what happens on my system. Hope this points you in the right direction.