There is no formal reason NOT to use the latter two examples, no ... but you're right, the former "sound funny," and that makes all the difference. It's a matter of prosody, and not grammar. Consider where the stresses / accents fall in each case:
You ARE what you EAT.
Your AC-tions re-FLECT who you ARE.
YOU'RE what you EAT.
Your AC-tions re-FLECT who YOU'RE.
The first two sound more natural; the latter two sound somewhat forced and awkward. The ear is often a good guide in such matters: if it sounds right, it probably is!