Using the Apple Battery Charger with non-Apple batteries
Apple Batteries are Rebranded Sanyo Batteries

According to engadget, the Apple supplied batteries are actually Sanyo Eneloop HR-3UTG, so it appears that's one option for buying additional batteries to use with the Apple Battery Charger.

Powerex Batteries Don't Work

According to the Apple Battery Charger Manual,


  
  Flashing Amber: May indicate any of the following conditions:
  
  The batteries haven’t been properly installed in the charger.
  An unsupported type of battery is in the charger.
  The batteries may be faulty or damaged and should be replaced.
  
  


With that information, I tried charging the Powerex 2500 and 2700 batteries but received a flashing amber light.

Looks like I need to buy some of the Sanyo Eneloop HR-3UTG batteries.