Probably the name of the folder isn't the plugin handle. Check inside the plugin's folder to see if the actual plugin folder is inside there. For instance:
forge@nys-production ~/nystudio107.com/craft/plugins (master) $ tree -L 1 craft-typogrify/
In this case, when the plugin is downloaded or cloned, the name of the folder is
craft-typogrify but the actual plugin folder is inside of this folder, and is named as a lowercase version of the plugin handle:
This is what needs to be directly in the
craft/plugins folder for Craft to see it.