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Experienced on haskell-mode-20151226.750/Emacs 24.5.1
After having customized a few indentation related custom variables via M-x customize-mode, I end up with the following init.el file:
(require 'package)
(custom-set-variables
 ;; custom-set-variables was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(haskell-indentation-ifte-offset 4)
 '(haskell-indentation-layout-offset 4)
 '(haskell-indentation-left-offset 4)
 '(package-archives
   (quote
    (("gnu" . "http://elpa.gnu.org/packages/")
     ("melpa" . "http://melpa.org/packages/")))))However, when restarting emacs with this init.el file those variables still show their default 2-value, and customize-variable tells me that the variable's state is
Hide Haskell Indentation Layout Offset: 2                                         
   [ State ]: CHANGED outside Customize.
   Extra indentation to add before expressions in a Haskell layout list.
Groups: [Haskell Indentation]
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