thats strange...i have MSreader in BIS, and all my ebooks on my SD card. when i load reader, it automatically finds all of the ebooks on my device...
check and see if your sd card is working properly (i.e., look in file explorer to see if your files are still there). if that's not the problem, check your .lit file to make sure it works (like open it in the desktop version of MS reader or something)...
also - do you see the help manual ebook that comes with reader? if not, maybe you need to reinstall...
edit: sorry...didn't see the other replies