I have had an issue like this on a laptop. it was caused by the windows language mapper. it had changed the keyboards layout to only include half the keys. i would check the language settings for your keyboard and make sure they are all for US, maybe even reset everything in that control panel.
if 2 keyboards fail then your right, its a software issue some where in the comp. boot up in safe mode and see if they keys work. if they do then its a service or program launching that is messing with it. if it remains the same then its a windows setting.