gdxf, to have the program "split the page in half" after you select the appropriate conversion mode, you have to switch the Sony Reader into Landscape. Do this by holding the Size button for 5+ seconds.
I've now updated the UI text a bit to make this step clearer. I must say, the UI screen asking and explaining layouts has had more evolution than almost anything else. Some developers take the darwinian view that you make a useable UI and not try to baby anyone or give it a second though (e.g. many of those working in unix/linux.) Meanwhile, other developers (like Apple) take it as their primary aim to remove everything that could take an iota of brainpower to figure out (the "simplest but no simpler" that keeps getting repeated to my ire). My opinion on this is that you have to keep trying to make the interface more and more intuitive, but then use that as an opportunity to make it more sophisticated in other places. This pushes progress and maintains the Flynn Effect
(no, seriously). Simplifying in order to complexify. For all the bad stuff that gets piled on microsoft, I think it's one of the few big developers that understands the inherent correctness of this approach.
The autocropping causing blank pages, though, sounds like a serious problem. Can you a) post your PDF and b) use the "preview" function and then copy all the text that you see get printed?* That last step will tell me some debug info, but only if previewing also gives you blank pages.
*To copy text from a CMD window, right-click on the title bar (the bar that has the X and minimize buttons), choose properities, and then enable QuickEdit mode. This lets you highlight text and copy it by right-clicking on it. Copy everything, even if you have to scroll up.