Contact Bill Hunt. He uses both PE and PR and will likely know the answer to this question. Most of us here only use PR and not PE, so this is difficult to answer without hands-on experience.
When you play your sequence back, do you hear audio? Or is it totally silent? If you do hear audio, the clips ARE in the timeline, but because of the way that Premiere Pro displays audio tracks, they may be pushed into "invisibility" off the bottom of the Timeline panel. Check to see if there is a vertical scroll bar at the far right of the Timeline, where the audio tracks are located. If there is, scroll down; your audio is probably there.
A bit of this might depend on the various versions, in which the Project was created, the version that you are Importing to, and variables, such as Themes, Instant Movies and any 3rd party Effects/Transitions.
With PrE 4 Projects, I have been able to Import those into PrPro 2.0, with few issues. If they were my Projects, they have come into PrPro 2.0 perfectly. With others' Projects, my "mileage" has varied. If they did use Themes, or Instant Movie, then things get very wonky. Some of their 3rd party (like New Blue Effects), have not come in properly.
I just tried to Import a PrE 8 Project into PrPro 2.0, but only got crashes. This indicates, to me, that there are version conflicts, just as with trying to Open, or Import, a PrPro CS4 Project into CS3. My guess would be that if one has an older, or contemporary version of a PrE Project and were Importing, or Opening in CS4.2, things would be much more likely to work fine.
As for your specific problem with the Audio, I would do as you have done, and then do a separate Import of those Audio Asset into PrPro, and just dragging them to a free Audio Track, aligning, as is required. You could leave the instances of the Clips, that do not play properly, you could Mute them in Audio Mixer (or similar with Enable, etc.), or just Delete them, after having used them as "alignment tools."
To date, I have not encountered what you are faced with, so do not have a definitive, easy workaround for it. Sorry.
Now, the first thing that I would try, would be to Open (not Import at this point) the PrE Project (PREL file) in PrPro. Can't recall if you need to manually point PrPro to the .PREL, or if it "sees" those initially. This will get you to a dialog screen, asking if you want to "Convert" the PrE Project to a PrPro one. Do so, and make sure to rename (maybe with "test," or just a numerical increment) the Project. Let PrPro process the .PREL. You might get some error messages, about missing Themes, etc. This will basically tell you what will NOT be converted. Same for Transitions and Effects. Once done, a Save, or Save_As will do. Next step would be to Import THAT PrPRo Project into a new one in PrPro. That might get you a better "conversion," than just an Import will.
Good luck, and please report your success.
PS - one cannot go the other direction. PrPRo Projects will not Import/Open in PrE, at least through PrE 4. You get an error message to the effect of "Fool, this is a PrPro Project. You need to drop big $'s and buy PrPro to Open this file. Fool." Imagine that error message being delivered by the actor, Mr. T.
Interesting observations. In PrE, the Audio & Video Tracks are related to one another, unlike the arrangement in PrPro. That could play a role here. Also, there are two "fixed" Audio Tracks, that can neither be moved, nor eliminated, Narration and Soundtrack. In my tests, I do not recall having anything on the Narration fixed Track.
The idea of Opening the PrE Project and letting PrPro "convert" the .PREL to a .PRPROJ file, might get one around the layout differences.
Also, the two fixed Audio Tracks, Narration and Soundtrack, seem to have certain odd limitations, restrictions, and just behavior. Users are often having issues with those. In most cases, just using another Audio Track (linked to a Video Track, whether used, or not), often gets one past this strange behavior. I'd love to hear from a development engineer for PrE, exactly what causes these two Tracks to exhibit that strange behavior. To date - no comment. All we know is that it happens, and the workaround is to NOT use them.
It could be that the OP has used either, or both. The "fix" might be to go back into PrE, move the Clips from either/both to other Audio Tracks, and do a Save_As, then Open THAT PREL in PrPro, or try Import again. I'd still go the Open, convert, Save_As route, and then Import that converted PRPROJ file into PrPro.
Just thinking here,
I was just able to import one of my old elements (version 7) into Premiere Pro, let it convert the file and when I dropped the sequence on the timeline, everything came through jsut fine, all editable, perfect. I don't know why this didn't work before or if I ws doing something a little different but this worked perfect!
Thanks for the suggestions!
I love Premiere Pro even more now. Now I have to talk myself in to Aftereffects......
Great news. If you encounter PrE Projects that do not behave, as one would hope, do check those Narration and Soundtrack Tracks - they are just odd ducks and don't "follow the rules," like other Audio Tracks.
Good luck, and I understand why you like PrPro better - I do too (but don't tell the PrE forum that... ). Glad that we could help.