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":
What is the key frame interval? And video and audio codec?
<!-- valid values are: videoKeyFrame, audio, enhanced. DEFAULT = videoKeyFrame -->
If you determine you need to re-encode the files you can use this guide:
How to encode video on demand content