Many words in Biblical Hebrew have a "pausal form", which differs slightly from its regular form in stress and/or vocalization. This form is usually used at the end of a phrase, although the regular form may also be used at the end of a phrase. For example, in the Song of the Sea natitha yeminekha tibla`emo ares, the word "land" appears as ares instead of eres. Similarly, in Ps 43:3 we read el har qodsheKHA [-shin-shewa-khaf-qames] we'el mishkenothekha, but in Ps 15:1, we read mi yishkon behar qodSHEkha [-shin-seghol-khaf-qames].
These forms usually appear with major disjunctive accents (silluq, athnah), but sometimes with minor disjunctives (such as zarqa, rebhia`). The word "you" (masc sing) is one of the few that have two pausal forms, a minor one aleph-pathah-taw-qames-he' and a major one aleph-qames-taw-qames-he', both with penultimate stress (i.e., stress on next-to-last syllable). The regular form (aleph-pathah-taw-qames-he' with stress on the last syllable) occurs 455 times in Tanakh (221 with disjunctive accents, 225 with conjunctive), the minor pausal 27 times, and the major pausal 52 times.
In the prayerbook, when it is not a quotation from Tanakh, the use of pausal form is usually a result of a movement in the late eighteenth - early nineteenth century c.e. to apply the rules of Biblical Hebrew grammar to the Rabbinic Hebrew of the siddur.
See Gesenius 29i-v; Weingreeen (A Practical Grammar for Classical Hebrew) p. 137; Jacobson (Chanting the Hebrew Bible) pp. 340ff.