eZ Publish 4.0.0 stable was recently released, so better to use this than alpha2 in the first place. But seems like this bug will be fixed in 4.0.1: http://issues.ez.no/12204
4.0.1 is expected to be there in January. In the meantime, you can use it from svn maybe? I didn't notice the second warning you got when I was replying you the first time: "Error initializing script: database error: No database handler was found for ''. Rather strange. I would inspect your [DatabaseSettings] block in all site.ini.append(.php) setting files.
I've tried a number of different versions of ezscript.php from the svn (perhaps not the right one - sorry don't know my way around yet!). All give the same error message (but on different line numbers obviously).
It turned out that safe_mode was on for php cli. The INI system uses file_exists() to check if an INI file is there, but this doesn't work when safe mode is on and will return false.