I'm having the same problem. WordPress is v3.1.1, FEE is v1.9.3.
I have editing turned on for post title, post content, and comment content only. With the WYSIWYG editor turned on, highlighting and tool tips work normally, but when I double-click the post content it disappears and never gives me an editor. Inspecting with firebug shows that the editor is there, and populated properly, but has
display: none; set inline at the element level. I am able to edit the post title and comment content as normal.
If I turn the WYSIWYG editor off, it appears to work fine in all three places.
I have no custom controls set on the WYSIWYG editor.
I can replicate this in Firefox 4, Chrome 10.0.*, and Safari 5.04 (all latest versions), on OSX 10.6.