I'm not sure how widespread this issue may be, so I thought I would just throw the idea/issue out there and see whether anyone thinks it is worth spending time on.
Basically the problem is that Java apps will break if they require Java 7 but jPortable 6 is installed, even when a local install of Java 7 exists.
So what I would suggest is that the launcher.ini needs a MinJavaRequired (and possibly a MaxJavaRequired for any apps that may only run on one or some versions) which will force the launcher to check the version of jPortable. If jPortable is installed and is a compatible version use that, else test for the existence of a local Java install. If the local install is a compatible version use that, else alert the user and not attempt to launch.
As I said, I'm not sure how widespread this issue would be as I don't know how many Java apps out there are moving to specifically require Java 7, but (once jPortable 7 is released) anyone who hasn't updated their jPortable will have these apps die silently after the splash screen appears.
Edit: Renamed my proposed JavaRequired to the more logical and flexible MaxJavaRequired.