Always always transcode. Use AMA as a means to view your footage, even log your footage, but transcode to MXF media when you're ready to edit. You can't kick out an AAF for audio mix from AMA media, and this issue you're having does happen quite a bit with AMA. You can transcode to DNxHD 145 or even 220 if you want to work at high res.
If you're using Media Composer 6, don't use AMA to bring it in. If you set your media creation settings to it's matching flavor of Pro Res and import it, it should fast import. Granted, only the Mac version of Media Composer 6 can do this, so if you're on a PC, DNxHD it is.
Los Angeles, CA
"We are the facilitators of our own creative evolution." - Bill Hicks