Just to bump this... I have a similar problem in Pythonista, except that my up/down arrow keys don't move from line to line at all unless I hold down shift (in which case, it selects the line of text between cursor positions). There is nothing wrong with the keyboard as I use it daily (e.g. to write this comment).
Other key combinations don't make sense, either. For example, option+down goes down two lines, while option+up goes up one line. Command+down jumps to the end of the document, but command+up seems to do nothing. Control+down and control+up seems to jump to the beginning and end of the document correctly.
The IDE is pretty tough to use in it's current state, unforunately. :/