I thought I'd update this with an answer to my own question!
The problem was the finite difference discretisations that I was using. They needed to be more complex to accommodate the variable properties -using an average heat diffusivity is just incorrect! The below image should hopefully show you how I dealt with the variable heat capacity and thermal conductivity. I used this as the basis of a FTCS explicit scheme, but I'm sure the principles hold for implicit schemes:

If that doesn't work try this web page (not mine!):
This only looks at a variable thermal conductivity type problem. It should be noted that problems with variable heat capacity or density would require an iterative process (linearising the non linear problem) as they rely on the temperature at the time-step t+1 as well as time-step t:
Hope this helps someone!
Chris