This may be obvious, but just in case anyone else ran into this problem:
I found that changes I made to the 'fck_config.js' file, particularly to the toolbar sets, did not appear when I refreshed the page with the editor in it.
To solve this, I had to go to tools->internet options :: General tab, and selected 'Delete files' in the "Temporary internet files" section. I then chose "ok", without checking "delete all offline content". Then click "ok" to close the "internet options dialog". Refresh the page and the toolbar changes appear.
I found that changes I made to the 'fck_config.js' file, particularly to the toolbar sets, did not appear when I refreshed the page with the editor in it.
To solve this, I had to go to tools->internet options :: General tab, and selected 'Delete files' in the "Temporary internet files" section. I then chose "ok", without checking "delete all offline content". Then click "ok" to close the "internet options dialog". Refresh the page and the toolbar changes appear.
RE: Toolbar configuration problem solved (v1.6)
RE: Toolbar configuration problem solved (v1.