It occurred to me after posting that that you were probably using the portable calibre from the Calibre website as opposed to the one provided by portableapps.com (which is what I'm using). The layouts are different - but still don't match the original bat file. However the key points are:
- set the environment variables to valid values (directories that actually exist)
- make sure you're in the right directory to call the calibre executable
- and that you call it the correct thing (calibre-portable.exe)
- make sure --start-in-tray and --with-library are called correctly.
BTW I used to have a clunky way of updating calibre portable, but portableapps.com have gotten better at not lagging too far behind so I tend to stick with their version now.