Windows Intune requires application deployment to be a silent (as in no user interaction) process. Sometimes working out how to do this can be quite hard. Richard at Windows Intunepedia has shared some information on this that I thought I would also share:
Steps to Deploy Adobe Reader X with Windows Intune
How to deploy Java 7 Runtime Environment (JRE) with Windows Intune
You might also want to look at http://silentinstall.org/ which can help wrapper other installers to ensure they are silent.
Thu, Jan 12 2012 7:39 PM