Hello there and welcome to the Wowza support forum.
What you describe is generally a problem with the source, the encoder. You can enable this Property so you can debug alignment:
How to debug AAC or MP3 timecode issues with Apple HLS packetization
Be sure to add "cupertinostreamingpacketizer" to /Streams /LiveStreamPacketizers
Also, can an you clarify what you mean by out of sync? How out of sync? Does it drift out of sync over time and is back in sync if you stop playing and start again? Is the stream out of sync when played back using Wowza Server?
What is the key frame interval set to? If it is very long that might be a problem. Try adding this Property to the Application.xml /Streams /Properties list: