There is an audio file of Reb Uri Weinberg zt"l (a fascinating person in Yerushalayim who passed away recently) discussing this very matter. (See here; scroll down about 1/3 of the way, and go to 19:55 in the audio clip.) Basically, he says that R' Wertheimer, who documented numerous manuscript specimens in the Cairo geniza and in other genizos in Yerushalayim, found that all old versions of this zemer had only six stanzas -- i.e., the ones spelling יצחק לח. The "expanded" version, with the acrostic יצחק לוריא חזק, was seemingly an invention of Shabsai Tzvi adherents. (I'm not sure whether Wertheimer was the one who first brought this version to light.) Reb Uri notes that in the original stanzas, the recurring words שבת מנוחה refer to Shabbos (as they are supposed to), while in the added stanzas, these words refer to Moshiach. [I don't know whether there is any solid evidence to back up this theory, however.]
;-)– msh210♦ Nov 27 '11 at 7:00