Well been doing some follow up, and playing with the msi transform.
CustomAction - installpublicjre - this is what calls the MSI for the JRE.
Using the executable switch of INSTALLDIRPUBJRE doesn't do anything when called from the MSI transform (adding as a property).
I made a new CustomAction , where I tweaked the JRE install command to msiexec.exe /i "[INSTALLDIR]\jre.msi" ADDLOCAL=ALL SDKSILENT=1 INSTALLDIR=[INSTALLDIRPUBJRE]
This works fine in the full gui execution mode, but not in silent mode (/q or /qb so far).
I tried adding it in to InstallExecuteSequence, but got errors, not sure the right place to put it to get it to run in silent mode.
Any thoughts would be greatly appreciated!