If you get this example warning when running the pRF:

(pRFFit:checkStimForAverages) !!! Average for Averages:6 component scan 5 does not match stimulus for other scans. If you wish to continue then this will use the stimfile associated with the first scan in the average !!! Do you wish to continue (y/n or a for Yes to all)?

It means that it thinks that scan 5 of the scans you averaged together has a different stimulus (e.g. wedges instead of bars) or something of the like. Since it is an average it has to figure out what stimulus to use for fitting the pRF and just picks the stimulus from the first scan. This could have happened for two reasons. One you might have mistakenly averaged a scan that does not belong. 2 there may be slight differences (off by a volume or so) in the recorded stimulus (due to when the volumes were recorded etc). The 2nd is not a problem, the first is. Look through the errors carefully to see if you can determine which is the case. It should tell you if it is a minor difference.