The following bug has been logged online:

Bug reference:      4006
Logged by:          David Schweikert
Email address:      [EMAIL PROTECTED]
PostgreSQL version: 8.3.0
Operating system:   Linux
Description:        pg_ctl assumes that all config files lie in
data_directory
Details: 

pg_ctl doesn't work if you put postgresql.conf in a different directory than
the database data files. According to the documentation, this is however
considered a good practice: 
http://www.postgresql.org/docs/8.3/interactive/runtime-config-file-locations
.html

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