I recently started a project and used the automatic stitching.  Sitcher put them all together except a few, and I manually stitched those together.  Once everything was to my satisfaction, I redner a tiff for editing in photoshop.  I did everything needed there and loaded the panorama.  I then rendered for a Cubic QTVR and that's my problem.  The panorama starts out by viewing the floor.  Then when you rotate around, the axis is continually wrong.  I've tried to align the panorama, but this really doesn't work.  

Hi C!
 
Possibly when you rendered from your original Stitcher set-up you had the camera looking at the floor? You mention a TIFF render -was this a spherical or cubic? If it was spherical, the correct orientation should be apparent in this output - cubic file output (i.e. the six faces) would not be so apparent.
 
Check your camera position in Stitcher when you render. What you see should be what you get.