> I can confirm this behavior.  It's been that way for some time.  You can still get it to work by clicking on a folder then using the keyboard to select multiple >files, but it's not nearly as user-friendly as it used to be. 

I am very interested in this "selecting multiple files with keyboard" I havn't been able to figure out how to do that.
Could you provide more information on how to ?

I just found this post just today.
I have noticed this issue myself, find it quite frustrating I am considering going back to an older jEdit just to run Buffer list 1.1.
Since Buffer List 1.1 allows close folder behaviour with jEdit version before 4.5.0.

I created a case for Buffer List beahviour on close folder in the Tracker back in May 2011.