Well... Nobody followed up on this. I've been beating my head against it all day, WHEN SUDDENLY.... I read the FAQ...
I realized there is probably a shadow function breaking things... Indeed, there was. I had both the RST and RTB installed. (University gives me all toolboxes. Yay?).
The problem I was having matches the one Jack was having, too many 'zero crossings'. Turns out that there is an angdiff function in the RST which was taking over the one supplied by the RTB.
Uninstalling RTB (for now) allows me to proceed on my merry way. Everything works a treat. Hurray!
So, Jack, It has been a year since you were messing with this. If you need it, try the command "which angdiff" from the command window. If it gives you something from the "Robotics Toolbox for Matlab" then your problem and my problem are the same.
Best of luck to you!
Craig