I have deployment for an application that is set to install at login. However configuration manager appears to treat a restart of the computer as different then if a user logs off then back on again. How do I make the application deploy install whether the users restart then log in or log off then log in?

Doing anything at restart is problematic at best because the ConfigMgr client agent isn't started yet.

Your best bet for this, depending upon exactly what it is, is to use a scheduled task.

I can't I have to do it at log in or off as this is the only time that the user does not have applications open that need to be closed.  It is working except for config manager sees a restart as different then a log  off.

No, ConfigMgr does not see a logon at start up any differently at all. As mentioned, ConfigMgr is *not* running at startup so it can't do anything at all.

If your challenge is to deploy software and ensure old versions (or dependencies) are not running, then running at startup is an inconvenient work-around at best. You should prompt the user to close those apps/dependencies. This can be done with the PowerShell Application Deployment Toolkit:

http://psappdeploytoolkit.com/ (or something similar).