I ended up starting again, I can only assume that it was something to do with the widths of the columns. I found this post which was useful.
In the frameworks section I decided to try a few. The first I tried was Zurb Foundations Ink, because I have used Zurb Foundation in the past. However, their supported clients wasn't comprehensive enough for my liking. They make no mention of the differing browsers, and in my opinion that matters. I've done a lot of testing in the last month. I will test it more thoroughly when I get time, at least they offer a version that works responsively in Gmail which doesn't use media queries.
Wanting something that worked on all platforms out of the box I tried Email on Acid's responsive template. It looks great, and I use Email on Acid to test, so I thought they would have it solved. Their website is full of useful tit-bits. However, their template didn't work in Safari and had the drop down issue I had initially started with. They don't claim it works there, but being as they offer a testing service, I had hoped it would work on all the platforms they use.
Then I moved onto AntWorts solution. That worked in my initial tests, and I found it remarkably easy to adapt to my needs, eventually adding additional columns using their methodology which was clearly explained in one of the templates.
My final template has 1,2,3,4 column grids which work responsively part fluid part adaptive. My advise to people in the future is to start with this boilerplate, I redid my whole template from scratch and it took half the time I have spent trying to troubleshoot a different boilerplate to start with.