I had a similar issue with CS4 and XP 32. If Premiere’s focus is lost the app locks up when returning. Premiere would then re-conform the audio into the same folder that was previously done, appending a -1, -2 to the file name.
I finally fixed both issues by deselecting “Write XMP ID to files on import” AND “Enable clip and XMP Metadata Linking” in Preferences>Media.