Sunny, where I must look for that?
Control Panel > Forum > Module settings, at the bottom. Please check the status of the option, so that I could understand the issue better.
I don't need to hide threads in subforums, I need hide duplicates from main section.
Exactly. The option doesn't hide threads in a subforum. The option hides threads of a subforum from the pages of its parent (main) forum. Which, as far as I can see, is exactly what happens on your forum and what you want to fix.
I'm not active on the forum anymore. Please contact other forum staff.