When you use Compressor to make the Pro Res file set the Audio settings in the Encoder tab of Compressor’s Inspector to PCM Linear, 48kHz, 16 or 24 bit. That’s what all professional NLEs expect to see. Setting the audio otherwise invites all sorts of not-so-good results, particularly, when encoding your final H.264.
John
MacPro 8-core 2.8GHz 8 GB RAM OS 10.5.8 QT7.6.4 Kona 3 Dual Cinema 23 ATI Radeon HD 3870, 24″ TV-Logic Monitor, ATTO ExpressSAS R380 RAID Adapter, PDE enclosure with 8-drive 6TB RAID 5
FCS 3 (FCP 7.0.2, Motion 4.0.2, Comp 3.5.2, DVDSP 4.2.2, Color 1.5.2)
Pro Tools HD w SYNC IO & 192 Digital I/O, Yamaha DM1000, Millennia Media HV-3C, Neumann U87, Schoeps Mk41 mics, Genelec Monitors, PrimaLT ISDN