On the Minoan Language blog, Andras Zeke counters my entry against a prefix *i- in Minoan with a new idea that the morpheme in question was a separate deictic instead. Clever, however only I-QA-*118 (HT44) ~ QA-*118 (KH 10) and I-DA-MA-TE (AR Zf1) ~ DA-MA-TE (KY Za 2) are available as evidence for this vocalic utterance, only significant if we assume that the two items of each pair have identical meaning. The pair YA-SA-SA-RA-ME (TL Za 1) ~ A-SA-SA-RA-ME (PR Za 1) only suggests a consonantal onset but this then is poor evidence for a purported morpheme that's independent of the word it precedes. Instead, if we assume that the pairs with I-/∅- are proper, the disappearing initial *i- is likely an unaccented vowel prone to syncope. This leaves just YA-SA-SA-RA-ME ~ A-SA-SA-RA-ME to explain, which isn't likely to be due to some disappearing morpheme, there one minute and gone the next.
In Prefixes in Minoan, I alluded to the Proto-Aegean phonotactic constraint against word-initial *y- which is evident not only in Minoan but in Etruscan as well. Of the 1504 words and names logged in my Etruscan database, not a single one shows an underlying word-initial /j-/. There's no question to me then that Etruscan phonotactics simply barred the glide from word-initial positions altogether. The apparently random alternation of YA-SA-SA-RA-ME ~ A-SA-SA-RA-ME in Minoan can be most parsimoniously explained by the same constraint. Given this feature in the language, symbols for YA and A would naturally be interchangeable in word-initial positions, as well as the pairs YE/E, YU/U, etc.
Aegean languages aren't the only ones to do this and I'm starting to see an interesting pattern around the Eastern Mediterranean. Egyptian too wrote ỉ (for consonant /j/) in places where /j/ no longer existed. So while the name of the god Amon was spelled out as ỉ-m-n in the vowelless script, the name was pronounced *ʔAmúna in the second millenium BCE (hence Coptic amoun). In other words, like I suggest for Linear A, Egyptian script wrote phantom glides in word-initial position while having developed a phonotactic constraint against word-initial /j/. More on this in Egyptian writing systems and grammar [pdf] by Shawn Knight.
Only recently did I have a brainwave about Greek and its development from Proto-Indo-European (PIE). Many IEists historically have noted that PIE *y- becomes either h- (PIE *yēkʷr̥ 'liver' > ἧπαρ hepar) or z- (PIE *yes- 'to seethe' > ζέω zéō). I never thought of this innovation in the context of this Minoan constraint rule before but I should have thought of this earlier in hindsight. Perhaps this is food for thought?
Then there are the hints in Anatolian languages of a possible similar constraint that I have to look into, at least where *ye- is concerned. All in all, there appears to be a geographical pattern of linguistic areal influence here with Minoan at the center.
 Münchener Studien zur Sprachwissenschaft, Issue 62 (2006) (see link): "However, the lack of any sure reflexes of */ie-/ in either Palaic or Lydian precludes the possibility of certain CAnat. status for this conditioned yōd-loss. (MELCHERT AHP 1994a: 75, KIMBALL HHP 1999: 361-2)."
 Melchert, Anatolian historical phonology (1994), p.75 (see link): "Hittite, Luvian, and Lycian give evidence for loss of initial */y/ before */e/. There are no certain examples for */ye-/ in Palaic and Lydian, so attribution of this change to PA must remain tentative."
 Woodard, The Ancient Languages of Asia Minor (2008), p.42 (see link) concerning Palaic: "The absence of examples of initial /y/ is surely accidental, but the lack of initial /r/ is systematic, as elsewhere in the ancient Anatolian languages." (identical to Melchert's statement in 1994:206).