Hi Graham.
Sorry to hear you are having problems. I took the liberty of registering you, and reporting the symptoms you described on the bugtracker:
http://issues.jalview.org/browse/JAL-1203
I think the problem may be due to the java version running on your machine, since the OSX distribution relies on the native java. Could you attach the console output file to the bug so I can see what version of java Jalview is running in and what errors are being reported ?
You should see a file called output.txt file in the directory where you installed Jalview (see the FAQ - http://www.jalview.org/faq#bug ).
Jim.