If you look up the word gloss in an English dictionary, you get two  for the price of one (typically labeled gloss1 and gloss2)—or three for the price of one if you check the cross-reference to gloze. Gloss1 and gloss2 come from totally different, etymologically  unrelated sources but their paths have intertwined over the years, merging (for some at least) in the expression to gloss over.

Gloss1 is ultimately from (West) Greek glossa (γλῶσσα)  (‘tongue [the organ],’ hence  ‘language, hence ‘obscure or foreign word [i.e., obscure word in a language or word in a foreign language]’). In Late Latin, the borrowed term glos(s)a had the sense of ‘a word needing explanation’ and, by extension, ‘explanation for an obscure word’ (whence glossary, a collection of such words with their explanations, which generally consisted of more common synonyms in the language or, later, translations into a second language with which the reader was presumably more familiar). Late Latin glosa naturally evolves into Old French glose, though Antoine Furetière in his monumental Dictionnaire universel françois et latin of 1771 evenhandedly reports an alternative derivation: “The word glose comes, according to some, from Greek γλῶττα, tongue [langue], because a glose serves to explain a text, as the tongue makes the soul’s feelings [sentimens] known through the medium of the word. One can also, Macri says, derive this word from Latin glos, which signifies a husband’s sister, and is considered a sister under the Law, because a glose is like a sister to the text.”

Furetière glosses glose as an “explanation of some obscure words in one language by more intelligible ones in that language. Also, a commentary that one makes to explain more intelligibly and at greater length an Author’s text, whether in the same language as the Author or in another language. It’s also used familiarly to refer to certain critical comments or details that one adds in reporting events or news of the day [Se dit aussi familièrement de certaines critiques, ou additions qu’on fait sur les événements & histoires du monde].” About the verb gloser, he has this to say: “To add a glose to an Author, to the pages of a classical Author, where space has been left between the lines to receive the glose. In addition, [gloser] means to add something to a story one is relating to make it nicer [plus agréable] or more entertaining [plus divertissante].”

English gloze basically assumed these meanings when it borrowed the word from Old French at around the end of the thirteenth century adding some of its own, most notably ‘flattery, cajolery.’  (There is some controversy over the origins of both  flatter(y) and cajole(ry): flatter seems originally have meant ‘to smooth (with the flat of  your hand—i.e., to stroke’) and may reflect the same root, ultimately, as platitude; while cajole originally meant ‘to shriek like a [blue]jay, like a caged jay’ about whose derivation the OED concludes its discussion with an uncharacteristic punt: “But the working out of the history must be left to French etymologists.”) The notion that a gloss for a word appeared in the text below the word that needed explanation—between the lines, as it were—is a plausible origin of the expression to read between the lines, though other derivations have been suggested: from the practice of writing the intended message in invisible ink between the lines of an otherwise innocuous letter, or embedding the message so that to decipher it you have to read every other line of the text and ignore the rest.

In the mid-1500s, gloze underwent a sort of lexical mitosis resulting in the retention of the original gloze and the creation of it’s alter ego gloss (gloss1). The (now archaic) noun gloze (which for a time was spelled both glose and gloze before the latter spelling eventually won out) had the senses of ‘comment, note; flattery; deception’ and as a verb,  ‘to interpret, comment on’ and ‘explain away.’ Gloss1 assumed the classical sense of ‘marginal or interlinear notation to explain an unfamiliar word’ and, by extension, ‘definition, explanation’ in general, casting off its previous vernacular senses (now assigned to gloze). The spelling of gloss reflects both the classical Greek and Latin and quite possibly the influence of the “other” gloss, gloss2.

Gloss2 arrived in English more or less at the same time as gloss1, but on a different boat: Gloss2 (which as a noun means ‘shininess of surface’ and as a verb, ‘to cause a surface to shine’) seems to have come from Scandinavia/Iceland from nothing that lexicographers have been able to pick out for sure from the lineup of Germanic suspects but whose parent is pretty clearly an Indo-European root meaning ‘shine’ or the like, the source of such words as gold, yellow, glow, glass, glitter, glisten, and glide.

Some say that the smart money is on gloss2 as the gloss that shows up in the expression to gloss over, i.e., ‘to give a facetious or disingenuous explanation for something,’ to which may be compared gild the lilyto gild ‘to cover with a thin layer of gold,’ hence, ‘to give an often deceptively attractive or improved appearance to; to gloss or gloss over.‘  (Compare the definitions at  http://www.thefreedictionary.com/gloss+over and http://idioms.thefreedictionary.com/gloss+over.) On the other hand, gloss1 has its backers too, and there are still others who prefer to hedge their bets. After all, by the time gloss over showed up in English (in the seventeenth century), gloze, gloss1, and gloss2 were all alive and well and living comfortably in the language, spelling was still a bit fluid, and  the written sources aren’t always all that clear about which word was actually being used, especially when the sense, then as now, was to explain something in its best light skipping over any of the unpleasant details. So, for example, http://dictionary.reference.com/browse/gloss lists gloss over under both gloss1 and gloss2 and, with the impartiality worthy of a latter-day Furetière, lets the reader make the call.