Anyhow, after tearing my hair out for a few hours I managed to work out what was causing the problem, switched editors temporarily and viola, fixed!
I spent the day testing out all of the minifier plugins/extensions listed here and this was the ONLY one that pruduced results worthy of any note. The main goal for my client was to reduce the load time of their page. Using JCH Optimize reduced the page load time by a staggering 50% :)
JCH is a breeze to set up, has plenty of options (even for the advanced user) and so far I can't fault it.