it is rather confusing that the profile activating by checking corresponding checkbox in the MavenProject tree affects the goals executing, but doesn't affect synchronization, and vice versa - the profile activating in MavenSettings/Import tab affects the synchronization, while the goals are executed without profile using.
probably these 2 settings should be synchronized - if profile is checked in Settings dialog, it should be shown checked in tree also, and affect both project synchronization and goals execution, and vice versa.