You have clips in Pr that are dynamically linked to Ae compositions, correct?
If so, an instance of Ae will start when Pr opens that project because it needs the information from Ae. Ditto for the AME. Hence the 2 Ae instances.
Dynamic link can be very slow, so if you have a complex comp in Ae that you are trying to export as part of your Pr project, you will experience longer than average wait times. Unfortunately, unlike your bank, you can't set AME to call you back and not lose your place in the queue.
If you haven't dynamically linked anything in your Pr project to Ae, then something else is going on that needs investigation.
The audio stuff may be as simple as waiting a little while for the audio to conform. Check the lower right corner of the status bar in Pr to see how such things are progressing.
... View more