clones want to align themselves along their Z axis, probably your objects are aligned along the Y axis (they point up?) if so just do + or - 90° P in the Transform tab, nothing else. It won't help to choose an Up Vector with that shape unless it's origin's rotation is odd.
it's just a choice they had to make at some point. It's like why is Y the up direction and Z into the screen (in the perspective view)? That's the way it mostly is now but earlier on it seemed like half and half (with the programs I saw anyway) and that's really just 'were the developers looking at a Front view or a Top view all the time when they were deciding'. The IGES format still has a "Swap Y and X axis" in the prefs but that's the only one now (of C4D's available formats).