I've had some problems with that in the past with some PDFs, even in portrait orientation. One workaround I came up with was to create annotation lines just above and just below the text. This prevented the auto-cropping from stepping over this line. You can reduce the opacity of the lines so that they are not particularly visible (don't remember if 0% opacity works or not).
Equivalently you could draw a box annotation around the whole page, but I never had it over-crop the sides.
Kindle Touch has a completely different PDF renderer (they used Adobe RMSDK before) so I don't know if it has this problem. Of course KT does not do landscape at present...