I am not sure about from a project as I've always rendered to a file first but I can tell you that if you render a Wav separately, put your video in to WShop and choose the separate audio file from the AUDIO TAB it will work.:thumbsup:
As I was also having problems with audio interruptions I've tried TMPEG which works well but gave the same problem with audio.
Only snag with this shortcut being audio - video synchronization, easily resolved by adjusting the length of the audio track by 2 or 3 frames (shorter I think) before rendering to Wav.
I personally do not see any video quality improvements in using Tmpeg software in my short trial time but I might purchase anyway since so cheap and it is claimed to be excellent.