Leia a pam_env.conf (5) manpage.
Acredito que você precisa adicionar chaves ao redor do nome da variável no lado direito:
GRADLE_HOME=/etc/gradle-0.9-preview-3
PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:${GRADLE_HOME}/bin"
(Possibly non-existent) environment
variables may be used in values using
the ${string} syntax and (possibly
non-existent) PAM_ITEMs may be used in
values using the @{string} syntax.
Both the $ and @ characters can be
backslash escaped to be used as
literal values values can be delimited
with "", escaped " not supported. Note
that many environment variables that
you would like to use may not be set
by the time the module is called. For
example, HOME is used below several
times, but many PAM applications don´t
make it available by the time you need
it.