In case it matters, Office Toolkit is no longer supported, I don't think that we ever did any work to make it CS3 compatible, and certainly didn't do any to make it CS4 compatible.
Now, on to the issue at hand. Extension Manager has a bug in it where it can't/won't make any edits to the Dreamweaver menu system. There is no rhyme or reason to why this occurs, but it does on occasion. The only why I've seen this issue go away, is to follow do #12 on the following page. However, you may want to try 4, 10, and 11 prior to 12 as 12 wipes out all of your installed extensions: