I won't upvote because it's not answering the OP's question, but I have the same problem with Eclipse. Timelines always show the old stuff on the left, and the compare screen should too.
The same issue here - presenting changed file on the left pane is very user unfriendly. I would love to know where this can be changed.
One more note to my previous comment - you can vote for the Eclipse change here: bugs.eclipse.org/bugs/show_bug.cgi?id=213780
I could not find the "Swap from and to" button in Eclipse Juno. Is it still there?