I had the reverse problem as described: first load worked fine in Mac OS X Safari, but changing the grid with all new items caused them all to stack in the top left corner. Further, waiting for ready event and setting CSS height & width on our elements didn't fix it.
On our site, we have categories of data that display in the masonry grid, and only one category shows at a time. A user could switch the category at any time and trigger an AJAX request to load in the new data. In latest Safari (9.1, 10) and browsers like Chrome, we could simply do this when changing the category to swap in all new elements:
// domData is HTML string from the server
// IMJS is our global variable that we use for globals and lookups
$("#divTemplateCategoryName").after(domData); // insert new HTML
var elementsToAdd = $(".grid-item-template-info"); //select the elements
IMJS.MasonryGrid.masonry('addItems', elementsToAdd); // tell masonry to add them
IMJS.MasonryGrid.masonry('layout'); // tell masonry to layout again
However, in some versions of Safari that wouldn't work, and we had to do this instead:
// domData is HTML string from the server
// IMJS is our global variable that we use for globals and lookups
IMJS.MasonryGrid.masonry('destroy'); // destroy the grid
$("#divTemplateCategoryName").after(domData); // insert new HTML
InitMasonry(); // re-do our entire masonry init
Because I don't have the time to track down every browser version that might be affected by this bug, I switched to the latter method for all browsers.