I also found that a project file gets caught up on the parameters of the irst song or sound imported or recorded into a project. I once turned a project into a template. I thought I could use the setup for future projects, all I had to do was delete regions and replace with new sounds or files; however, the template retained the information from the original first file that setup the project. The problem was that when I would bounce the a stereo file (mp3/aif/etc), the bounce time lined up NOT with my new song or files BUT with the original songs/files. So the answer for me was 2-fold. Understanding the way LPX sets up a project once you have imported/recorded/created so first sound, I had to, one, just use a new project every time (seems obvious and easy) and , two, create a template that never has a sound in it (so it's never creating a preference profile). This fixed my bounce issue. So it wasn't a bug rather I was trying to do something that LPX doesn't know how to undo inside a saved project.
