Are you still experiencing this issue?
What version of FMS are you using? (Build number?)
I tested with the packager, downloaded seperately as 'adobe_f4fpackager_4_5_1_windows_x64.zip', its version is: "F4fpackager version 4,5,1,484".
I tested against one packaged with FMS version "Adobe Flash Media Server 4.5.0 r297"
The audio popping was an issue with FMS, precisely when content was fragmented using JIT which is fixed in FMS 4.5.2. I am not sure you should be seeing this when fragmenting through the f4fpackager.
Can you please send me the URL that you are using to access the Adobe sample video - sample2_1000kbps.f4v ?
Also, please update your FMS to the latest 4.5.2 from here:
And let me know if you are still facing the issue.