I've not used MCEBuddy a ton but did you try checking "disable cropping" under conversion task settings? (Hit the advanced button to show them after selecting the task & hitting change.)
To convert single files you click Add on main screen then browse & select the file but sounds like you found that already. Not sure you can select a file if you have existing conversions waiting in the monitor folder.. Think you'd need to change our monitor
path temporarily but I could be wrong.
Bill