I can't be as thorough as Drifus, but I can confirm the problem. I installed CCleaner 3.19.1721 (64-bit) tonight, ran it, opened Thunderbird, and saw a message pane had been added to my layout. I also noticed the quick filter bar had been added. I removed the quick filter bar and message pane, closed Thunderbird, ran CCleaner, opened Thunderbird, and saw the message pane and quick filter bar had been added again. I removed them and closed Thunderbird.
I looked at CCleaner's Thunderbird settings and guessed that session might be the culprit. I unchecked session, ran CCleaner, opened Thunderbird, and the message pane and the quick filter bar were not there, which was the way I had set them. Session appears to be what adds the message pane and quick filter bar.
CCleaner Thunderbird options checked when problem occurs
Internet Cache
Internet History
Cookies
Download History
Session
Windows 7 Professional SP1 64-bit
Thunderbird 12.0.1
Jon