Have You Checked That The 64 bit IE9 Functions Right?
Many are unhappy with IE9 64 bit.. Although it may work exactly as you want, I would make sure that the 64 bit version works for the websites you need it for....PLUS....I would also check to make sure that leaving Java enabled in the 64 bit version actually disables it in the 32 bit IE9. Since there's only one Java control in the "Start-Control Panel" section, enabling it there may cause both IE9 versions to work..
Of course, since you probably have both 32 bit and 64 bit version of Java installed in "Programs and Features", you might try uninstalling the 32 bit version of Java there, which should prevent the use of Java in the 32 bit version of IE9.. Give it a try.
Hope this helps.