Sounds like a player issue. I don’t think there is anything you can do in Wowza to help. The standalone VLC handles seek in vod rtsp streams from Wowza.
If you want to stream to a browser plugin, it would be better to use Flash or Silverlight. You can do RTMP to Flash, or Flash HTTP (SanJose) streaming with an OSMF player. And of course you can do Silverlight HTTP (Smooth) streaming to Silverlight player.
Some player links:
This is Wowza example Flash player that supports Sanjose streaming:
OSMF:
http://www.wowza.com/downloads/forums/OSMFPlayers/OSMFPlayers.zip
Strobe (will do SanJose)
http://www.osmf.org/strobe_mediaplayback.html
Flash Media Playback (hosted, easiest) (will do SanJose)
http://www.osmf.org/strobe_mediaplayback.html
https://www.wowza.com/docs/how-to-use-strobe-media-playback-with-a-wowza-media-server
Adobe OSMF sources
http://opensource.adobe.com/wiki/display/osmf/Open+Source+Media+Framework
You can also use Silverlight, this is the Wowza example Silverlight player:
Silverlight:
http://www.wowza.com/downloads/forums/smoothstreamingexampleplayers/SmoothStreamingExamplePlayers.zip
And Expression 4 Encoder has Smooth player templates.
Richard