I have the same problem, even though I have left the apple tv on over night in Media Player within the grid view in my movie folder to ‘cache’, it still only loads each cover on a grid view when you scroll down. Even then, changing the view to list, its clear that it is still fetching the data fresh every time!
I’m very disappointed as I only purchased the atvflash software (2 weeks ago so I assume I’m running the latest version you refer to?) to bypass itunes but still retain the features of meta data and cover flow.
As a backup I have tried using XBMC but this doesn’t even display the covers after collecting data (and yes I have followed the convoltuted instructions)
Any help appreciated.