Did you add "-t <token>" to the command line, that starts the agent?
In your bamboo web-ui click "Administations > Agents > Install Remote Agent" and follow the instructions: Command line should contain "-t": java -jar .... -t <your-token-code>
If this does not help, add your token code to the wrapper file on your agent: ~/bamboo-agent-home/conf/wrapper.conf Find line: wrapper.java.additional.3=