Change the layout? Lock the panels? I can't quite picture your setup in my head (in terms of how you are even able to work with everything zapping back and forth al lthe time), but it should be easy enough to resolve this little problem using the methods I described.
It'll help if you use the right terms. The Timeline panel is a "panel"; the Effect Controls panel is a "panel". If you have them docked together, they share the same "frame".
I can't image working with the Timeline panel and Effect Controls panel in the same frame.
Why don't you use one of the standard workspaces, such as the one named Standard? It has these two panels in different frames so that they don't jump in front of each other.
So I guess this is just the way it is. If the effect controls panel is behind the timeline panel in the same frame, the effects control panel will always jump to the front when I try to change a filter paremeter in the timeline. Bummer.
The UI layout I have presently is by the far best I have found for my workflow (except for this issue). And the effects controls panel does not fit well in my other frames (its tab is too wide when it includes the name of the file that the filter is being applied to, and because of this, blocks the names of the other tabs in the frame). This seems to fall under the category of car lights that automatically come on at certain times, even when the driver doesn't want them to. Sometimes it is a help, but for me, I prefer less automation and more personal control.
I figured out a work-around. I undocked the effects controls panel so that it was all by itself and made it smaller than the timeline panel. And now when I am working on my timeline and changing filter parameters, the effects controls panel stays hidden unless I double-click on the name of a specific filter name in the list of filters listed connected to each layer.
Interesting concept for a useful UI. You did what Mylenium suggested, unlokced the panels and changed your layout. In the olden days, the UI was not nearly as flexible and could not accommodate easily the whims of individual users. You are fortunate to live is the days of dockable panels, versatile panes, enclosable frames, and portable HUDs. You can even save this layout of yours and carry it with you to other CS4 or CS5 installations.
You want a cool AE layout? Run three Apple 30" displays!
I guess that in a way I did do what he suggested. And yes, it is nice to have so much flexibility with the UI. I just wish the effects controls panel did not auto-jump to the front of its panel when effects parameters are changed in the timeline. This is a well-intentioned-but-not-helpful-for-me feature and because of this, I am not able to include both panels in the same frame.
Now if the UI would just stop freezing (and staying frozen) so much. I asked a question about this in this forum, but no one has been able to answer it yet: http://forums.adobe.com/message/2953599#2953599