I jumped into your site and did some investigating and I think I’ve pinpointed the issue. The logo/brand link is set to take people to a section. And when that link is current or has the current selector applied there is no padding on the link:
As you scroll down and leave the section you’re linked to the element loses that current state. On that class, minus the current selector, there is a padding added which is causing the logo/brand to jump.
If you make that padding consistent between the two states that should take care of your issue!
Let me know if you have any other questions and I’ll be happy to assist you further!