Maybe we should look at the problem a different way. The original situation was in reference to .jar files. From what I can tell, those should be related to Java applications and my not even have any "System" files that would be checked by the SFC.
Also, from my XP days, I do not remember SFC being very reliable if run after some updates might have been installed that changed some system files. Maybe SP3 made that better, not really sure. I started running it on my old laptop, and was asked to insert the DVD also.
I would probably try reinstalling whatever application that is supposed to be using the .jar files. Do you happen to know which ones are causing the problems?