You probably just need to update MMF2 (doesn't require Developer version).
Previously, you had to be using the non-HWA build to create Java apps, but that is no longer the case (although you still can't use HWA effects in a Java app).
You should have the following options:
* Stand-alone Java Internet Applet,
* Stand-alone Java Webstart.
If you have MMF2-Developer, you will also have an option for Java Mobile (J2ME).
Tip: If you intend to build a Java app, select that build option before you even begin - that way it will stop you adding any extensions that aren't supported by the Java build (rather than waiting until you try and build the game, and giving you an error message).
Problem is, the Java Mobile Runtime is going to be outdated quite soon now that Androids and iPhones are saturating the market. I don't think Clickteam are going to do too much more with it.