Install applications after install of Yosemite 10.10.2

I erased my HD with disk utility and then did a fresh install of Yosemite. Now when I try to install the programs I had previously, legal/licensed programs or even just a basic install like Firefox downloaded from the Internet, the install fails. The installer eventually goes to not responding in Activity Monitor. I never get prompted to agree to AUPs or anything. I was able to install iPhoto from the App Store, but all other install attempts for things like Adobe Reader, Java etc.. all fail.
I was able to install Firefox and Photomatix Pro by "dragging to the Application" folder.
I did notice in System settings - Security and Privacy that Apps downloaded from is set to App Store and Identified Developers, this should be good. But I also clicked the lock icon and it just says Authenticating. I should be prompted to put in the administrators password.  
What is stopping me from installing basic applications like Adobe Reader?

thank you for the quick reply Glenn.
I did do the permissions repair, but failed to restart. I should have known that needed to be done. Thanks again!

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