I've tried the usual black magic of with and without _definst. with and without a slash in front of the first directory (4). I've tried moving the smil up to the /content directory and out of the sub directories.... Dozens of permutations. On some of the permutations I get: Error #2032 (which is an HTTP 404 no found error)
btw, you would see those WARN lines with INFO level debug, which I recommend you revert to.
What do you see in the log files when you try to play the sanjose URL? You can see by running Wowza in stand-alone (/bin/startup.bat) mode instead of as a service, so you can see log output in the console.
How are you playing back the sanjose stream? You need a OSMF player. Take a look at this player: