I would suspect that the "flat" end of the stud threads into the block. Is the thread length on that end of the stud a bit shorter? Also, the threads on the block end are designed for a closer fit than the standard thread on the nut end. Likely, that "fit" wears some over time with every removal and installation, but in theory when being installed correctly it will take more effort to screw them into the block vs. the other end (incorrect) end.
As to the lead washers, their purpose has been argued about on here for years.
The consensus seems to be that they provide a sort of "lube" to prevent the steel nuts from gouging into the cast iron head, making for a more smooth/accurate tightening/torquing of the nuts.