Well I've kinda answered my own question but I wouldn't mind some comments on the solution.

I've created entries in the init.d directories for both JReceiver and tRio but to get them to work I've had to copy in JAVA environment variables into the scripts as the variables do not appear to be set at this part of the boot process. The big problem with doing this is that if these variables are ever changed by the java package, these scripts will break again.

Anyway, i've put these statements in. Do I need all three of them? I'm just too lasy to try each one by themselved!

export JAVA_BINDIR=/usr/lib/java/jre/bin
export JAVA_HOME=/usr/lib/java/jre
export JAVA_ROOT=/usr/lib/java