By '..latest java..' what version is that? Is it 7u11, or if on 6 it would be 6u38?
Let's assume 7u11 was installed and a 6uX release was previously installed, and may still be one the system. Also as "JavaFX2.1 Runtime" is in the error that is seen lets presume JavaFX 2.1 was installed on the system.
From Add/Remove Programs in the Windows control panel do you see an application(s) called JavaFX? By uninstalling JUST the JavaFX application, does the prompt no longer take place? Please do not uninstall any other Java installations you may have at this time! I want to understand if this one single removal resolves the issue.
I believe JRE+JFX installation, should prompt to de-install old JFX rather than confusing users
Indeed, that would be ideal in the general case.
Alas Oracle cannot tailor to the general case; there are "less than professional" (IMO) software solutions out there that depend heavily on very specific versions of Java and by extension also JavaFX 2. Such a software product would not work anymore if the runtime installation would just remove the outdated JavaFX runtime in favor of the new one. You could make the removal optional of course, but that is only really "safe" when dealing with people who want to know what they are doing - not the common "next next next" person.
Managing software installations is still the responsibility of the person managing the work station, which includes cleaning up old junk when it is not needed anymore. When that moment has arrived can only be determined by humans, not (dumb) installer software. Of course the actual managing of Java installations could be made a whole lot easier with some specific tooling...