I have Google Analytics set up on a site and it is tracking traffic correctly. I set up Webmaster tools and linked the accounts. It's been running for a few days now and says it's correctly linked. However, it's not showing any clicks from search. But Google Analytics is showing that about 65% of my traffic is coming from Google. Do you know why Webmaster tools would show no clicks from search?
Check your default URL in case that's not set to the current sub-domain/protocol. It may be you're getting clicks but they're not being attributed in the Search Console.
Search Console data is also 2-3 days behind the current date. It can vary a great deal and even be delayed up to a week.
Otherwise, Search Console should actually be more accurate due to the sampling technique used by Analytics.