It can be a setting issue or a compatibility problem. Nevertheless, there are a number of ways we may make it work.
Please make sure that you have the most recent versions of both Premiere Pro and Audition.
The multitrack settings you want in audition, match it with the sequence settings you have in Premiere Pro. I hope you’re taking advantage of Premiere Pro’s export to Adobe aaudition feature.
If you select Edit in Audition by right clicking on your sequence in Premiere, and then select Sequence to preserve the multitrack structure. You’ll also be able to modify the audio in audition while preserving all the track properties.
If the problem still occurs, you could potentially export each audio track separately from Premiere before importing them into Audition to execute multitrack editing.