But I don't get the connection to the frequency setting. That issue still persists, right? Without any frequency specified, they still go right up to 500?
I dropped it all together, reinstalled fresh version of RPI and cgminer. Now it listens to me! 
I remember messing with system commands, somehow I set cgminer as a system command and set it with parameters.
If you save a config file but then don't want to use it, you gotta find it and delete it.
It will be saved in the directory of the user who ran cgminer.
If you use sudo then the user is root, not the user that typed the command.
That's what 'sudo' means.
When you pressed S+W it told you where it saved it.