I have problems with correct alignment of the closing parenthesis in
cperl-mode. For example consider the following Perl code:

my $a = func1(
    Module::test()
  );

my $b = func2(
    test()
);

my $c = func3(
    Module::test(),
);
We see that the closing parenthesis is not correctly indented for func1,
but for func2 and func3 it is correct.

In cperl-mode-hook I have

(setq cperl-indent-level 4)
(setq cperl-indent-parens-as-block t)
(setq cperl-close-paren-offset -4)

It seems to me that this behavior is related to the newest version of
cperl-mode. I am using Emacs 24.4 on Ubuntu 14.04, and the cperl-mode that
came with the installation
(/opt/emacs24.4/share/emacs/24.4/lisp/progmodes/cperl-mode.el.gz) is
version 6.1 of cperl-mode.

I then tried to install cperl-mode from ELPA using Emacs 24.4 package
manager (list-packages), and it turned out that it gave me version 5.23 of
cperl-mode which also indented the closing parenthesis correctly..

M-x emacs-version:

GNU Emacs 24.4.1 (x86_64-unknown-linux-gnu, GTK+ Version 3.10.8) of
2015-01-11 on hakon-ThinkPad-Edge-E540

I built Emacs 24.4.1 from source, using with `--with-xft` option to
configure.

Best regards,
Håkon Hægland