I reverted back to 6.2 to avoid this behavior

I found that the CM window was full-sized in any case after upgrading to 6.3, so I just resized it, and it appears to stay resized. So I guess it's unexpected behavour after the upgrade but easily remedied.

I also encounter this same problem whenever my laptop resumes from sleep - The CM window appears onscreen, and each time it has become full-sized to take up the whole screen.

And a separate, but probably related, issue is that after booting into Windows (i.e. a cold start, not resuming), Task Manager considers ClipboardFusion to be an application that is running in the foreground (it appears in the 'Apps' list on the Processes tab) rather than being a background process, which it subsequently becomes after manually invoking and then closing the CM window.