I'm actually having the exact same problem. I've checked the deployment type - Installation behavior is set to "Install for system" & Logon requirement is "Whether or not a user is logged on".
My scenario is I'm trying to change an existing task sequence that currently installs MS Office 2010 to instead install Office 2013. I remove the 2010 application and try to add the 2013 app (which is located in the same place as 2010) and it's not shown as an option.
Any other ideas as to what could be causing this?
