Matthew,
I did some testing on WSS 3.0 with the CEWP and I can click on the Rich Text Editor or Source Editor buttons, which does open the correct dialog, when the jQuery Panel web part is wrapping the CEWB or not. Additionally, the default open the tool pane link works as expected when a new CEWP is placed onto a page...and then wrapped by the jQuery Panel Web Part.
In your first post you were referencing the CQWP (MOSS)...is this the OOTB web part you are having trouble with? Or is the CEWB (WSS) the web part which is giving you trouble? I would be glad to give you a call to discuss...so I can get to the bottom of this issue. Just let me know how you would like to proceed. Thanks.