My best suggestion is to Merge the clips in the same project you'll be editing in. Does that work?
Going to try, but here is my workflow and have not encountered any problems until this last P/U days footage. I've been doing things this way because I found having all files in the project was causing it to crash constantly when I was working. I have a new I7' processor IMac with 24 gigs of RAM. And since Premiere does not allow you to have multiple projects open at the same time (Wish this would change. Avid and FCP both allowed multiple projects) I have to do things this way.
Pre-workflow Project File
Label all Video and Audio files to match Scene #'/Takes
Set in points on all video and audio to reflect slate
Working Project File
Import only Merged Clips into Project. Either via import or copy/paste
Now I've done this workflow from just about the very beginning. Deleting all of the original source video and all audio clips from my working project so only my bins containing my merged clips remain. Have had no problems and edit has been smooth. Did a pickup day last week, followed same steps as I've done in the past, imported the merged clips into my working project and the clips have the audio set to none by default. Now once I go into the sequence I can manually set it and it's there but I cannot play audio in the source monitor which is how I edit, there's no reason I should have to go back to the crappy FCP way of editing doing the copy and paste from a sequence.