[ESS] indentation

[Terry Therneau]

 My ess customizations (of which the most important is an indent level
 of 4 --- old eyes need the help) stopped working with a machine
 upgrade.
 Old: Ubuntu 8.04 LTS
 New: Ubuntu 8.10
         ESS downloaded from a CRAN mirror (Iowa State)
 The customizations are a block of lines in my .emacs file
 (require 'ess-site)
 (setq ess-tab-always-indent nil)
 (setq ess-auto-newline nil)
 (setq ess-indent-level 4)
 (setq ess-brace-offset 4)
 (setq ess-close-brace-offset 4)
   etc

Here is the real puzzle: If I look at the customizations via   " M-x
 customize-group RET ess" I see all of my values.  Each one says "this
 has been changed outside" and gives my setting.
 If I start a new buffer "test.R" however, they are not in effect.  The
 buffer mode is marked as  (ESS [S] [none]), so S mode is being chosen.

Within the new buffer a query for the value "C-h v ess-indent-level"
 gives the following text:

 ess-indent-level is a variable defined in `ess-cust.el'.
 Its value is 2
 Local in buffer temp.R; global value is 4

 Documentation:
 *Indentation of S statements with respect to containing block.
 You can customize this variable.


 -----------------------------
 Great -- I have set the global default, but it does not apply to
any given file!

Any insights would be appreciated.
   Terry Therneau