This was mentioned over on AegeaNet yesterday ... there's a recent ph.d. dissertation online:

Hellemans, Geert, Etude phonetique et graphique du [j] (jod) en grec mycénien

Obviously it's in French, so here's the English abstract:

Our study deals with the pronunciation and spelling of Mycenaean, the oldest Greek dialect known to man (ca. 1400-1200 BC). More specifically, it is investigated in which word positions the [j] sound occurred and to what extent this sound has been systematically recorded on the clay tablets in Linear B script. For each word position (e.g. word-initially or in intervocalic position) the relevant material is presented and interpreted, in dialogue with the literature already present. Moreover the phonetic result of Indo-European [j] in Mycenaean is reconstructed, whenever it deviates from the inherited [j] sound.
History of e.g. French, German or Dutch spelling shows the existence of variants, some ofwhich have gradually disappeared, while others have been generalized. Our study demonstrates that such phenomena are also apparent in Mycenaean spelling (e.g. in the notation of material adjectives). Originally the spelling was predominantly phonetic; gradually it became more standardized and more conservative, but never entirely uniform.
Our study aims to contribute to the description of the Mycenaean phonetic system. Special attention in this respect is paid to linguistic variation: various types of pronunciation and spelling variants are traced and commented on (the available data from Knossos and Pylos are being continuously compared; additionally the specific character of the documents from the Room of the Chariot Tablets at Knossos is studied). Our theory on Linear B as a mixed spelling system, finally, transcends the primary question of our study and may inspire other Mycenologists and language historians.

Please feel free to pass along more online dissertations that you are aware of ...