"In an Ugaritic text concerning the abode of Kothar-wa-Ḫasis, the god of artisans, the word kptr occurs: kptr ksu ṯbth ḥkpt arṣ nḥlth, 'Caphtor is the throne of his sitting, Ḥkpt the land of his inheritance' (UT, `nt VI:14-16). The passage seems to preserve a memory of a connection with Crete as the home of their crafts; Ḥkpt may be another name for Crete or one of its regions. Economic texts from Mari speak of Kaptara, and an Akkadian text from Ugarit refers to ships arriving from Kapturi. C. H. Gordon had raised the question whether the words kpt-r and ḥ-kpt may include some morphological elements, a preformative ḥ- and a sufformative -r, leaving kpt as the basic word (Ugaritic Literature , p.23 n.1), and relating this to Egyptian kft-yw. But the persistance of r in Hebrew, Akkadian and Ugaritic forms, plus the fact that final -r could become -yw by phonetic decay (see CAPHTOR II), rather support kptr/kftr as the original word."So we can conclude with some degree of confidence that the name sounded something like *Kʰaputar, give or take some variation. For the sake of argument, I will suggest this specific form and what follows is a whole lot of speculation. I personally think of speculation as a necessary tool in the learning process, used to invigorate new paths of research and I always strive to improve my arguments with facts and evidence or to eventually abandon them, whichever logic guides me to do. However, for those overly evidentialist sorts that find any speculation without evidence too distasteful to even express, you may be spared reading further.
I'm very interested in the Minoan language and have been pursuing a hunch for years that the likeliest relationship it has is to the 'Etrusco-Cypriot' languages (Etruscan, Lemnian, Rhaetic, Eteo-Cretan and Eteo-Cypriot) whose epicenter lies in Western Anatolia and Cyprus, formerly known as the kingdoms of Alashiya, Arzawa and Assuwa. I also have a hunch that by 1400 BCE, Minoan had become a dead language but still used in ritual while, in the everyday world of the commoners, a mix of Greek and Etrusco-Cypriot languages survived on in Crete.
If I take the name *Kʰaputar for granted, I'm reminded of a plural suffix *-r that I see in the Minoan Libation Formula sometimes marking the word *una 'libation' (written syllabically as U-NA-; in the sequence U-NA(-RU)-KA-NA-SI, *una(-r) kana-si '(we) bear libation(s)', compare Etruscan -r [animate plural], un 'libation' and cenu 'brought'). Without this ending, we're tentatively left with a singular word *kʰaputa. Wild imagination may lead one to see similarity between it and the Latin-derived word 'capital' however this leads to another interesting mystery: Where does Latin caput 'head, summit' come from?
Some etymologists try very hard to make caput a Proto-Indo-European word. However, it's unclear to me why anyone would be so determined to force the word to be PIE given the meager basis. At most, they're reduced to label it vaguely as a 'regional term' or an 'Italo-Germanic innovation' which only skips over the problem of how the word came to be. However, let's try a new idea. Let's suppose for a moment that this odd word is entirely non-IE and a loan from a theoretical Old Etruscan word *χapuθ (> (?) Late Etruscan *χafθ), lent also at some point to Germanic (hence Old English heafod). At this juncture, I think many readers here might predict where I'm going with these crazy ideas.
Is it just possible that the word for 'head, summit' in both Minoan and Etrusco-Cypriot during the mid 2nd millenium BCE was originally *kʰaputa? From there, *Kʰaputar 'The Summits'(?) would become the word for the entire Minoan region, perhaps in connection to the Horns of Consecration, a very sacred and prominent symbol undoubtedly related to the Egyptian aker symbol representing the sun both emerging from and setting into the two horizons.
Now naturally, these are so far just a delightful multiplication of hypotheses and fun wordgames to toy with while passing the toke around. I recognize that it remains incumbent on me to prove them with tangible evidence if I'm ever to insist this hypothesis to others. So, as always, I'll just have to see where these ideas take me.
 Mallory/Adams, Encyclopedia of Indo-European culture (1997), pp.260-261: kaput (see link).