I've done a quick brush up on CSS and solved my problem - see question for updated fiddle. Was a very simple one in the end, it probably looked hard due to my question hence why there were no answers from the community within the last 24 hours.
I hope my steps help someone else who's new to solving these types of issues, browsers have some great tools built in these days for trouble shooting.
Steps I used for solving:
1.) The first useful step I found was to inspect the element with internet explorer via right click on the page. Then use the right click option in the source it shows to copy element with styles. This gave me a smaller version of the html for testing which I saved into a standalone html.
2.) I started pulling out html elements that appeared unrelated and making the sample simpler. Once I pulled something out I'd refresh the html in IE and check what happened.
3.) When I had a simple html I saw the absolute positioning and the asterisk, I then did a quick google to find this stack question explaining what the asterisk does.
4.) I need to leave the absolute styling in so that isotope works, but I can specify relative positioning inside the isotope, I've done this by using the asterisk myself now I know what it does! :)
#chartFilters * {
position: relative;
}