When I run CC, just the first part which cleans out rubbish, it interfers with Thunderbird.
The Message Pane returns, despite me setting Thunderbird not to show the Message Pane,
Win XP Pro, Thunderbird 12.0.1
This has only recently starting happening.
This has been reported before, though I do not experience this. Try updating Thunderbird, I believe you're a few versions behind.
I just tested this.
Thunderbird / Session cleans session.json. Cleaning session.json closes open emails/emails in tabs and opens the message panel.
Using CCleaner v3.22.1800 and Thunderbird v15.0.1.