We've had this issue before, there are several potential causes:
1) Media cache is corrupt - Close Premiere and manually delete all files in Media Cache locations (can see location via Preferences -> Media Cache). Relaunch project and wait for it to re-conform all audio. If that doesn't work, it could be that Premiere is "remembering" the link to the old media file's waveform (or lack of). Try changing the name of the file on your hard drive and re-importing it to Premiere (or relinking/replacing footage). This will trick Premiere into thinking it's a brand new file and it will kick off the conforming process again.
2) You're mixing and matching stereo and mono files on a single audio track inside the nest. Instead, keep things on tracks grouped by stereo, mono, etc. Even better, in the Project panel, Modify Audio Channels of all your audio files and keep things all consistent (i.e. all mono) so you have more control for solo/mute and can see the waveforms more clearly per track.
3) Make sure no audio gain or effects are applied on the clips inside the nest. Only apply gain and effects at the top level (i.e. put the effects on the outside of nests, not on the contents inside).
4) Nested audio can get weird - is this a simple nested sequence or a multicam enabled sequence? If multicam, then in the top level sequence where the nest is being used in the timeline, you have two choices. For example, if you have a 2-track audio .WAV inside a nest, you can "point" to those two tracks from the master sequence by:
a) Modify Audio Channels (Project panel) the .WAV file as stereo and place on Audio Track 1 inside the nest. Then Modify Audio Channels (Project panel) the nested sequence to use Channels 1&2 to select the needed audio track in the master sequence
-or-
b) Modify Audio Channels (Project panel) the .WAV file as two mono tracks and place one on Audio Track 1 and the other on Audio Track 2 inside the nest. Then Modify Audio Channels (Project panel) the nested sequence to use Channel 1 for *both* audio tracks, and then use the Multicamera selector in the master sequence to choose which Camera Angle (aka which audio track from the nest) to point to. To do this, in the top level sequence, unlink video and audio of the nested clip that is not showing waveforms, right click on each audio track and choose Multicamera -> Camera X (pointing to whichever track your audio corresponds to on the inside nest).
5) If all else fails, try rendering the audio. I know, huge pain, but sometimes it's worth it. If it's a monster audio file or it'll take forever, then maybe consider using markers inside the nest where you can see waveforms to mark several key points, then those markers will be visible in the level above.
Hopefully that makes sense! We deal with nested multicam workflows all the time here, and lack of waveforms usually boils down to one of these things.
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