Is it live or vod streaming? What version of Wowza are you using?
Key frame alignment between renditions is a requirement. For live streams you can debug alignment like this:
For vod you can load them up in the scheduler and stream them live to debug as above. Also for vod, see this article on encoding for ABR:
You can turn on logging for all chunk creation by adding this Property set to "0" in the Application.xml /LiveStreamPacketizer Properties container (this is the one at the bottom, not at top where live packetizers are set)
It's hard to debug iOS switching. In some case there is evidence in the logs if you look at the rows of a c-client-id. You could use a Silverlight or OSMF debug player to some extent because switching either works or for any of the HTTP stream types.
Silverlight debug player: