The only potential cause of this that I can think is the font script taking longer to load, but odd that we can’t replicate it here, definitely not an issue with the theme else you would see this on every load.
I’d recommend trying a caching plugin such as WP Super Cache, which will cache the page and thus shouldn’t encounter an issue like that – give it a try?
When you get the issue, load up the browser console (usually under View, or Develop) and check for any errors. If you get any, post them here and I can advise.
Maybe it is a timing problem of a javascript code or css transformation. It is related to the “fading” of the font (headers and links) into the site. Maybe it also have something to do with the power of the computer. I use an older Macbook and I do not have the problem very often. My colleague has a much faster Mac and it happens all the time. But it is always only Safari, not Firefox. Not related to OS or version of Safari because we have the problem since about a year.