I set BAMBOO_HOME in setenv.sh, when I start Bamboo I get:

Bamboo home directory specified: .
There was an error creating the Bamboo Home directory. The most common cause is you haven't specified it.
To fix this, simply set the bamboo.home property in the file /WEB-INF/classes/bamboo-init.properties to your chosen bamboo home directory .

If I set via the properties file, all is well, so the setenv.sh / environment route seems to not work?

Resolution: This is a duplicate of BAM-14836 which was created first and has more votes. Closed in favor of that one.