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.