Hmm...I can't say unless you are using a different Style Template for the pages that the Compact Footer is not working. Go into your CP and look under Template Associations in Style Templates.
Along with the $Footer that you edited in public_common.pl file, you may also need to edit "sub StandardHTML" and "sub StandardHTML2". For these I couldn't use $Footer. Instead I had to enter the actual footer code in those two spots.
While I did my own Footers the concept should be the same as with drkknght's.
