I wonder if the reader.pref file is corrupt. It normally looks something like this:
#User preferences for Reader Booklet
#Fri May 27 17:58:37 GMT-06:59 2011
FONT_SIZE=25
DICTIONARY=The New Oxford American Dictionary
LINE_SPACING=2
JUSTIFICATION=full
LAST_BOOK_READ=/mnt/us/documents/Buddenbrooks The Decline of a Fa-asin_B004G60B6W-type_EBOK-v_0.azw
HORIZONTAL_MARGIN=40
FONT_FAMILY=condensed
Note that there is a Justification setting, normally it would be 'full' as above, but if it is missing, or there is some junk there instead, maybe it is applying 'center' as the default for all books that don't supply explicit justification style.
It is located in a folder named /system/com.amazon.booklet.reader. When your kindle is connected to your computer via USB you can open it with a text editor and have a look.
I believe that if you delete it, Kindle will recreate the file, so you could give that a try. I would make a copy before doing that however, in case you want to restore it for any reason.
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