I'd like to chime in to say I'm having the same problem since updating to Suffusion 4.2.0 with the welcome page on this site: http://www.theoldmarket.com/
The custom layout is as it should be if viewed in Firefox on a mac, but in Safari (and Omniweb and Chrome), the widget layout is erratic, it changes on a page reload, but rights itself if you adjust the window. We didn't have this issue with the previous version of Suffusion. Also, previously I had "no height adjustment" selected in custom layout, but now only the Jquery masonry option will actually allow 3 columns of widgets, any other selection makes the widget (a category query) span the page.
I tried disabling plugins, re-uploading Wordpress, and Drake, I tried the custom includes suggestion re widget height limits: nothing is working... so any other other suggestion would be greatly appreciated!