When adding your timer onto a page inside of ClickFunnels, you'll need to make sure that when adding the code, you select the '3rd Party Embed Code' option when adding the timer code onto your page/s.
Here's a support article from ClickFunnels that explains this (see Step 2, point 5);
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PS: Still got questions? Join our Official Countdown Hero Support Group on Facebook! You’ll be able to join and post your question in there and not only are your fellow Countdown Hero users in there helping each other out 24/7 but our support team are in there too.
(Heck, you might even find the answer to your question is already in there and you’ll get an even speedier solution)
Join the Group Here: https://www.facebook.com/groups/countdownheroofficial