This used to happen to me ALL THE TIME. So I finally went over to one of the production companies I work for and sat down with an editor to figure it out. We found 2 issues. The 1st issue is "Nested" files/sequences within Premier. If you're using this feature in premier and you try to export an omf for Pro Tools (it's a known issue that Pro Tools and Premier don't get along. Other DAW's may not have the same issue) it will never come out right. If nested sequences are used, you have to first export to audition (which comes with premier so it's no biggie), then export an omf from there.
The 2nd issue (if you're not using nested files / sequences) is Premier gives you an option to "encapsulate" the audio when exporting an OMF. If you don't select this option, Pro tools again, won't be able to open it. This encapsulates the audio WITHIN the OMF file. If you don't select encapsulate then Premier will make an OMF file (a map basically) and a separate "audio files" folder (all the audio files) - however because Premier (as you mentioned) DOES rename things whatever it wants, Pro tools doesn't recognize the audio pieces that plug into the 'map'. In other words the meta data doesn't match up....I know, it's screwy.
Also note that the OMF file will always come in all MONO tracks, so any stereo tracks will have to be converted back to stereo in PT, which is as easy as dragging the two mono tracks to an empty stereo track.
Basically I simply tell my clients the following before they send me an omf:
- when exporting an OMF, please be sure to select the "encapsulate" option
- If you're edit session has any nested files/sequences, pro tools may not be able to open the OMF. You may have to first export to audition, then export an OMF from there.
Hope all this info helps. Hopefully they'll fix it in an update in the near future.