Hello
I have experienced issue and I would like to share with you how I solved.
I rooted my device with the Western Flavor minimal root
https://wiki.mobileread.com/wiki/PRST...eaks#Procedure
https://wiki.mobileread.com/wiki/PRST...Western_Flavor
then for some reason I wanted to restore factory settings by using this process:
http://www.kb.sony.com/selfservice/d...nalId=C1024494
DO NOT DO THIS!
Otherwise some settings will remain from the Rooting.

For instance I was no more able to pup up the keyboard!
The correct way is
1) root
https://wiki.mobileread.com/wiki/PRST...eaks#Procedure
if you want to reset factory reset before you must
2) UNROOT
http://projects.mobileread.com/reade...estore-set.zip (and BTW you must use the same procedure of the rooting at the end, after execution of flash_reader.bt you must Hold the Home and Menu buttons together and while holding them turn on your READER. Once the opening book screen comes on, release the buttons.)
3) then if you want you can execute FACTORY reset!