If you don't need it to run in the standalone Flash Player (i.e. as a .exe, for example) then you're safe. It's just because the standalone Flash Player has no JavaScript capabilities, so it needs to run in a web browser for that.
As for the names: if you based yours on the existing buttons, which look like this, e.g
<togglebutton name="btn_mute" style="common mute"/>
you'll notice there's a
name attribute (with value btn_mute in this case). These names are used by the navigationbar plugin to attach event handler to those buttons. So if you use JavaScript to trigger anything if that button is clicked, you should remove that, to avoid side effects. If you're unsure and want feedback, feel free to post your XML (or at least a snippet of it) here.