Best just to view this fiddle in both Firefox and Chrome/Safari to see what I'm talking about.
Basically... it works fine with pixel margins in all browsers, but when the margins are percentages... Firefox holds true, while Chrome/Safari fail...
This is a jQuery bug, not Isotope specifically. Keep an eye on jQuery bugs #10117 and #10639. Hopefully this will be resolved in jQuery v1.7.2
Seems that it in turn is a Webkit bug (#29084). A hack/workaround was added to jQuery three weeks ago, and is slated for 1.7.2.
Closed as fixed with jQuery 1.7.2
src & test : add hackPercentMargin to getWH
fixes bug when margin is in percentage
All the hard work done by @mikesherov