I think I narrowed down a Safari problem to the pop-up pop-down function. The menu won't go back down and then the menu disappears completely, go to another site with the menu, the menu won't appear at all.
Can you check this is not just me?
You can test it on the Milonic example menus, when the menu disappears use the same browser window to go to your own site to see if your menu is not loading at all.
If you can duplicate this problem, we should send a bug report to Safari.
I opened a new window and went to the Milonic home site. Popped a bunch of menus and subs. Then I went to my site in the same window and all the menus opened and closed with no problems.