Check if you have this key in your registry :
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\FileExts\.bat\UserChoice
if you have one it means that the .bat extension is currently associated with notepad (or another program defined by the “Progid” key under this node).
Backup you registry and remove this .bat “UserChoice” node.
your .bat files should then run normally.