I'm not sure what version of ruby & rails you're using, but I tried using a similar setup as your yaml file and was presented with an error about bad parsing. I think that a key which has something nested underneath it cannot also have a value.
That said, I experienced similar behavior - the hash-based accessor for nested values set/returned the expected values while the method-based accessor returned the value from the file and did not get the updates:
# config/settings.yml
defaults: &defaults
thing1: 1
thing2: 2
nest:
thing3: 3
development:
<<: *defaults
2.0.0p247 :001 > Settings[:nest][:thing3] = 30
=> 30
2.0.0p247 :002 > Settings[:nest][:thing3]
=> 30
2.0.0p247 :003 > Settings.nest.thing3
=> 3
It looks like this could be a bug in the gem, which based on the issue list on github seems to be one of many with nested attributes.