Don’t know if you guys got to the bottom of this, but I came to this thread with similar problems.
I’m editing on a Mac Pro 6-core Xeon with 16GB of RAM, an internal RAID, and an AJA KONA 3G.
I have a Premiere Pro CS5.0.4 1080p Timeline with some ProRes QT, DSLR h.264 QT and an AIF music file.
As the timeline plays back the volume of the music track mutes in and out. When I export it as a standalone QT movie, everything plays back fine from the desktop.
I’m new to Premiere, and I presume that it’s not unusual for tracks to mute on playback if the system is getting bogged down.