I haven't ever formatted/initialized my File Store ever since I've bought my Pocket Loox 720 (some 14-15 months ago) and, when I started making some explicit tests to see how fast it is, I was really frightened to see it was about 30 (thirty) times slower to write to than after a reformat. Indeed it's worth reformatting the File Store in order to gain back the lost speed!
Please see
http://www.pocketpcmag.com/blogs/ind...3&p=521&more=1 for more info / the complete tutorial!