Pasted carriage returns ending up as br tags instead of new paragraphs — 3.9.1

This is a continuation of a discussion from this thread. I’m still having the issue after upgrading to 3.9.1 — created new thread per moderator request.

I’m trying to change how WordPress treats carriage returns in text that is pasted into the text editor (as opposed to typed in). In WordPress 3.8.3, it behaved exactly the way I wanted it to; in 3.9 and 3.9.1, all my paragraphs end up separated by line break tags instead of being rendered as new paragraphs.

I regularly need to paste from InDesign documents in which each new paragraph is a single carriage return. What I used to get, and would like to go back to, is this:

<p>This is paragraph 1.</p>
<p>This is paragraph 2.</p>
<p>This is paragraph 3.</p>

What I get instead is this:

<p>This is paragraph 1.<br /> This is paragraph 2.<br /> This is paragraph 3.</p>

… which is both unattractive and, I believe, not recommended semantically.

I’ve tried installing CKEditor, which accomplishes what I’m trying to do as long as I’m using my Mac, but doesn’t fix the problem when I’m using a Windows 7 machine (which is what all of our office computers are).

In WP 3.8.3, the “Paste as plaintext” button brought up a popup window with a “Keep linebreaks” checkbox that, if checked, rendered all pasted returns as new paragraphs (closing out the old p tag and opening a new one). This was extremely useful. Is there any way to bring it back?