El comando
\usepackage[english,greek]{babel}
hace que MikTeX 2.9 funcione para siempre.
Sistema operativo Windows 7
La salida es
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (MiKTeX 2.9)
entering extended mode
(C:/Users/x/AppData/Local/Temp/lyx_tmpdir.Hp3100/lyx_tmpbuf2/negreponti-1.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, afrikaans, ancientgreek, ar
abic, armenian, assamese, basque, bengali, bokmal, bulgarian, catalan, coptic,
croatian, czech, danish, dutch, esperanto, estonian, farsi, finnish, french, ga
lician, german, greek, gujarati, hindi, hungarian, icelandic, indonesian, inter
lingua, irish, italian, kannada, kurmanji, latin, latvian, lithuanian, malayala
m, marathi, mongolian, mongolianlmc, monogreek, ngerman, nynorsk, oriya, panjab
i, pinyin, polish, portuguese, romanian, russian, sanskrit, serbian, slovak, sl
ovenian, spanish, swedish, swissgerman, tamil, telugu, turkish, turkmen, ukengl
ish, ukrainian, uppersorbian, usenglishmax, welsh, loaded.
Editado:del comentario de OP, código pequeño:
\makeatletter \makeatother
\documentclass[11pt,oneside]{amsart}
\usepackage[iso-8859-7]{inputenc}
\usepackage[a4paper]{geometry}
\usepackage{amsthm}
\usepackage{amstext}
\usepackage{amssymb}
\makeatletter
\usepackage[english,greek]{babel}
%\usepackage[default]{gfsneohellenic}
%\usepackage[LGR,T1]{fontenc} %% LGR encoding is needed for gfsneohellenic
\makeatother
\begin{document} klkk \greektext γφγγ
\end{document}