Working with Presenter 7.0.2, on a windows machine using Powerpoint 2007.
PPTX files are still not working great. I had font problems,(bolding of text automatically), font spacing issues. As I moved through a presentation working in PPTX files was much quicker than working in a PPT file especially saving the file. I recommend that you build your presentation in PPTX files to take advantage of the newer features of Powerpoint, but then save as a PPT file for publishing the presenter file. I did come across some syncing issues that I created in PPTX that didn't convert over to PPT. Definitely watch over your published file to make sure syncing is correct. You might have to change the PPT file to get it correct.
BTW, I had a co-worker who couldn't work on the PPT file over the network from our server. This problem was fixed when we installed latest .0.2 update.
Best way to delete audio from a slide is to insert a new slide, copy the text and images onto the new slide, then delete the old slide. Resync the animations with audio if needed and then you are done. We tried deleting audio from the code and data file structure, but it didn't work, caused corruption.
Hope some of this helps others. :-)