Has to do with Multiple Processes
When running dual processors, or in the case of the P4's with HT you can set SETIDriver to run more than one process and that checkbox has to do with setting the affinity in such cases. To be honest, I have seen opinions split about 50/50 on whether or not it needs to be checked. I personally only have one machine in this configuration, and it is a true dual-processor being a pair of MP2100's on an Asus dual board, and I do have the affinity box checked and it has been running two instances of SETIatHome happily for over a year. I have never tried unchecking the box to see if it caused any difference.
SkyHook