First of all, which version of IE you are testing on. IE8 eg. doesnot support SVG and fallsback to Png. Guess your testing on IE9+
Browserdifferences is always a tough thing to handle. With SVG its even harder because you need to know the differences in browserhandling of the SVG elements. Maybe in IE the order of elements is different or there is an extra tag before it. You have to check that out in IE.
One thing i prefer when using SVG, maybe not relevant to this… but maybe usefull …is GSAP Tweenmax library. Allthough aimed at tweening and animation, their SVG handling is perfect.
Read this article about browserdifferences in handling SVG and how they tackle it. Might be usefull and inspiring.