GG01:
Paul,
If you upgrade to the latest and greatest you will see extra options at the bottom and those should help you out.
OK, I have downloadd the laest off Zen Cart's site, and upgraded the mod, but still can't get things to work right. For instance I just put through an order:

The points on the bottom of the order (1511) are correct, though the points in the side box (1711) are wrong (they are including the shipping price). Then when I go to admin > customers > Reward Points
It say the customer has earned 986 points? I haven't a clue what that relates to, it means 49.30 in money spent to earn that number of points.
Hmm, it has all gone a bit wierd since the upgrade. I am still using ZenCart v1.3.8.a
Currently, I have disabled the "Advanced Reward Point Calculation Rules" as I had been playing about with them and not getting anywhere fast.
I think something else has gone wrong :(