First I would NOT recomend clicking Run As Administrator at this point. Mostly because Windosws 7 is telling you that the executable command.exe was installed from the internet. This could indicate virus activity, which is a possibility since windows 7 does not ship with antivirus software installed, and most existing AV software must be uninstalled prior to upgrading and the Win 7 version installed after the install is complete. This leaves your system vulnerable to attack -- a silent one since no AV is installed.
Run a Virus scan against the executable first. if that is not the issue then I would recomend inserting the windows 7 dvd into the dvd drive of your pc, rebooting to the DVD, and running the automated repair utility. If you installed from a wim OR iso file, you will need to burn the image to a dvd first, as you must runt the repair utility before the OS boots.
If you used a WIM image, and your dvd burning software does not support WIM images, you can Use the IMageX utility in the Windows Automated Installation Kit located at microsoft.com/downloads/details.aspx?FamilyID=c7d4bc6d-15f3-4284-9123-679830d629f2&DisplayLang=en .
If you have not used imageX before I would strongly suggest downloading the third party ImageX gui , GImageX http://www.autoitscript.com/gimagex/ This will let you mount the imaged you ned, and create the iso, so you can burn the dvd, so you can fix your installation of Windows 7.
Before all of this, of course, back up all your data, as the last resort would be a Format, re-install and restore.
All of this assumes, you have a legitimate licensed copy of Windows 7, and not a pirated copy downloaded from a warez sight that preinstalled malware for you.
Hope that Helps!
Also, WinKey+R does not run in admin mode, and running from the search in Windows Seven does indeed work, I use it all the time.