I am assuming the data is directly comparable. The more important question is, are there any hardware differences in the units other than SD card vs CF card?

I'd prefer to buy a used one to save some cash, but if there is a significant difference, the new one may be a better choice.

I suppose I'll have to wait till everyone is home from SoW :]

 

There is no difference. The hardware is slightly different, but the firmware is the same. I have the old one, Fil has the new one. I've analyzed his data. No difference.