The startup behaviour hasn't changed since it was introduced (a while ago). It's always been the case that you need to either re-install LimeWire again or drop a link to LimeWire in the startup folder (and add a -startup parameter to the command) in order to do a startup, in addition to checking 'Start On Startup' in the options in LimeWire. Yes, it's clunky, but we didn't have an easy way of making a link to start LimeWire through Java. At some point we'll come up with a better way of doing it, but it's not really a huge priority now.