I'm not sure what you mean. If I comment the page reloads, the book stays where it was (say ch5) but with my comment present and I can then just go on to the next chapter. It could be a difference in browser. However, I find it easier to I write my comments in a wordpad file open alongside the Authonomy window and copy and paste them in when I'm ready. 
I do the same thing, but instead of Wordpad, I use a regular, old fashioned pad. Like, literally, a notebook. Then I type my comments out in the comment box.
(*riiiing, riiing*)
Oops, excuse me for a moment . . . .
Hey, I just got a call from the dark ages and they're wondering why I still use a pen and paper. Cool.