For anyone trying to do this I managed to crack it without downloading anything extra:
I needed to change 2 things:
1 FlowControl was set to hardware for some reason, I had to explicitly change it to software
2 Weirdly, although I could see the serial port and communicate with it on hyperterminal ONLY over COM8 I HAD to use COM1 within Matlab to get a reply. This is a pain, as my matlab GUI I've written uses a spectrometer on COM1, so hopefully I don't get a hardware clash on the serial ports. Anyway, that's a separate issue.
Thanks for you help!