According to the Wikipedia Manual of Style, these are some rules on the matter (I'll paste it):
When showing the source of an acronym, initialism, or syllabic abbreviation, emphasizing the letters that make up the acronym is undesirable:
Incorrect: FOREX (FOReign EXchange)
Incorrect: FOREX (foreign exchange)
Correct: FOREX (foreign exchange)
If it is necessary to do so, for example, to indicate the etymology, use italics: FOREX (from "foreign exchange")
Specifically, do not apply initial capitals in a full term that is a common noun just because capitals are used in the abbreviation.
Incorrect (not a name/proper noun): We used Digital Scanning (DS) technology
Correct: We used digital scanning (DS) technology
Correct (name/proper noun): produced by the British Broadcasting Corporation (BBC)
So: don't capitalize if the words are "common" and capitalize if the acronym refers to proper names. See also page 81 in this document.