Okay, so you mean when seeking.
Can you explain your set up?
What is the key frame interval?
What are the video and audio codecs?
What players are experiencing this issue?
Is the issue only on a certain stream? or on multiple streams?
Is it pretty consistent or sporadic when this happens?
Are you doing adaptive bitrate streaming?
It could be that the key frame interval is to high. For seek to work, Wowza needs a key frame every 10 seconds. You can increase Wowza key frame tolerance by adding the following property to the MediaReader/Properties section in [install-dir]/conf/[application]/Application.xml. It looks like this:
Another suggestion is to try adding seekTarget Property to the Application.xml /Streams /Properties list set to "enhanced":
If you determine you need to re-encode the files you can use this guide:
<!-- valid values are: videoKeyFrame, audio, enhanced. DEFAULT = videoKeyFrame -->
How to encode video on demand content