It can be hard to tell the difference; since they often look very similar.
In both cases, white text (or a white grid test pattern) on a black background is the easiest way to reveal the flaw.
CA is caused primarily by the lens: and generally varies across the image (ie, it's more pronounced in certain areas of the image - often the corners, where the lens is at its weakest - and less so in others). Zooming and changing focus also tends shift it's appearance. It's often evidenced as purple fringing.
Misalignment is caused purely by the panels: for this reason, it usually will not vary across the image - so one corner of the image will be misaligned in the same manner as the center and opposite corner. It's also limited in color to either the panel colors, or a combination of two panel colors (so if red is misaligned, you'll get red fringing throughout the whole image. If it's red as well as blue, it'll be purple-fringed throughout the whole image; etc).
So the consistency of said fringing is probably the most reliable means of telling the difference.
BenQ W1070 Projector; Xtreamer Ultra 2 (running XBMC on OpenELEC) via Sony STR-DH540 AVR with Boston Acoustics SoundWare XS SE 5.1 Audio. MediaBrowser3 for Mobile Streaming.
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