The JNLP file specifies which java version to run with.
By default (with my installation at least) on the system config page it specified the java versions as “1.6+;1.5+”.
Changing this to “1.6;1.5+” fixed the JNLP and made FPMI run under java 6 instead of java 7 and made me look like a genius.
Hopefully this will help others…