Lock the video track, drag your audio out point, unlock the video track.
Depending on the Export settings (both from AE, and PrPro), the block sizes on some Audio formats will differ very slightly, than the accompanying Video file. The differences are usually very slight, but can cause problems, similar to what you are encountering.
What are the Audio and Video formats and their settings?
Not saying that this is your cause, but it happens fairly often, and will usually show up in Encore.
If you hold down the ALT key, you can trim the audio or video portion of a clip without affecting the other portion.
Sweet! I never knew that!
All these tips solved my problem. But just FYI, it's RED .R3D files with embedded 24-bit/48KHz mono tracks.