I took a peek at it, and there seems to be some sort of bug. You can see in the screenshots below that, even though the same class name is displayed, the padding on the right is different. Unfortunately, I’m thinking you might need to re-create the nav menu.
It’s not as bad as it sounds. I’ve had bugs before that required me to recreate the nav menu, and, after I stopped being pissed off, it only took a few minutes.
If you really don’t want to, then I’d try removing all suspect positioning values from every element in the main navigation, and then re-apply positioning just to the Nav-links.
Here’s how I’d remove the positioning values:
(Click on the blue value, then click Remove this style.)