You might be interested that there seems to be a clash between JHEP3.cls version 3.1.5 (from http://jhep.sissa.it/jhep/help/JHEP/TeXclass/tools_JHEPlog.html) and the ifpdf package. I think both packages use variable \ifpdf, which clashes.
When I compile:
\documentclass{JHEP3}
\usepackage{graphics}
\author{Kuba}
\date{14/12/2012}
\abstract{ble}
\title{ble}
\keywords{ble bel}
\preprint{10932}
\begin{document} ble ble \end{document}
I get
Package ifpdf Error: Name clash, \ifpdf is already defined.
However, when I replace all \ifpdf in JHEP3.cls to \ifpddf, all \pdftrue to \pddftrue, and all \pdffalse to \pddffalse, it works fine!
I will also write to inform JHEP.
Including \let\ifpdf\relax (as suggested in Package ifpdf Error) does not help, because an error message like Extra \fi \begin{document} appears.
Do you have another/better idea, how to deal with this?

JHEP3.cls. – Martin Schröder Dec 15 '12 at 7:32