I also had this type of problems when I used Pc2Amiga some years ago. You will need to tweak the options to minimize these transfer errors. Try to raise the "retries before fail" value. I don't remember if there's a baud setting for parallel cable too, if so try setting it to a lower value.
Also, have you selected the correct cable in the settings (4- or 8-wires cable)? If your cable is the special 8-wire one you must be careful to plug the ends to the correct computers, one side is for the Amiga, the other for PC. I once have built one of these cables, but I couldn't manage to make it work, so I switched to a standard 4-wire laplink one.
The difference between the KS2 and KS3 versions should be explained in the manual, if you don't have it then download the program's archive from Aminet.
Varthall
