
The comma indicates that "彼女は" is the subject of "わからない", so this sentence rather means "She doesn't know what she really wants." (For this meaning, I'd prefer to say "彼女は、自分が本当は何が欲しいのか分かっていない".)
If you omit the comma and change "彼女は" to "彼女が", it will become a natural translation of the English sentence. (See http://tatoeba.org/eng/sentences/show/119472)
I also propose an alternative "彼女が本当は何が欲しいのか、私にはわからない". This is less ambiguous and sounds natural enough.

your suggestion sounds much more natural to me
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linked by marcelostockle, February 1, 2012
edited by marcelostockle, February 10, 2013