Have the same problem in Opera and Opera Next. The way I found to reproduce was this.

• Wipe everything in APPDATA\Opera
• Launch the browser (Opera thinks is a fresh install)
• Visit a site that uses flash (YT will do)
• Flash loading properly
• Activate click to play
• Reload YT, click to play is in effect
• Add YT to white list. Click to play still in effect
• Reset the option to default - run automatically. Click to play is still in effect.

That said there's little to do about because this proves that

a) Click to play is broken
b) Apparently so do whitelist. Worth checking too.

Hope you guys find this info useful.