From OG 10 - SC#205 -

The peaks of a mountain range, acting like rocks in a streambed, produce ripples in the air flowing over them; the resulting flow pattern, with crests and troughs that remain stationary although the air that forms them is moving rapidly, are known as "standing waves.

A) crests and troughs that remain stationary altough the air that forms them is moving rapidly, are
B) crests and troughs that remain stationary altough they are formed by rapidly moving air, are
C) crests and troughs that remain staitionary altough the air that forms them is moving rapidly, is
D) stationary crests and troughs altough the air that forms them is moving rapidly, are
E) stationary crests and troughs altough the air that forms them is moving rapidly, is

After elimnating 3/5 ... please help explain the difference between the last two remaining choices...

You forgot to say which three choices you eliminated. By process of elimination (heh) I'll assume that you eliminated ABD based on the mismatch between singular subject ('flow pattern') and plural verb ('are'), leaving CE.

C is better than E for at least 2 reasons:
(1) There's better parallelism between the 2 principal parts (crests...stationary and air...rapidly)
(2) incorrect use of 'although' in the subordinate clause: 'although' has to separate a CLAUSE (with a verb) from another CLAUSE (with a verb). 'Stationary crests and troughs' doesn't have a verb.