It's expected behaviour. See here
When bash is invoked as an interactive
login shell, or as a non-interactive
shell with the --login option, it
first reads and executes commands from
the file /etc/profile, if that file
exists. After reading that file, it
looks for ~/.bash_profile,
~/.bash_login, and ~/.profile, in that
order, and reads and executes commands
from the first one that exists and is
readable.
So only the first readable one counts.
As for which you should use, it's up to you - unless there are corporate policies or something else that creates a specific one, or relies on a specific one existing.