The Geneious PAUP plugin (http://www.geneious.com/plugins/paup-star-plugin) works with commercial releases of PAUP* up to and including version PAUP* 4.0b10. You will need to have your own licensed copy of this version in order to run the plugin.
The Geneious PAUP plugin will not work with alpha releases of PAUP* up to and including 4.0a147.
However, the author of PAUP* has recently made available temporary "test version" command-line binaries of PAUP* 4.0a148 for Windows and OSX. These binaries are compatible with the latest Geneious PAUP plugin (1.3.0).
The PAUP* 4.0a148 binaries for Windows and OSX can be downloaded from http://people.sc.fsu.edu/~dswofford/paup_test/.