You should be fine in terms of how settings were selected. 4K and above will use the half setting (the half debayering) while the 2k will use full. Everything will get resized to 1920x1080 (or I assume, as ProRes doesn't have the bitrate to handle anything larger than 2K since it's really an intermediate format). 5K, unless you set some crop marks may result in shadow boxes.
Chances are you just aren't use to how Redcine-X selects and adds items to the export queue so you may have selected from the full bin twice or maybe you double loaded a bin.