Actually, I take that back. I don't see any correct way for PerlIO_setpos() to end up calling fread().

My first guess is that the pointers in a PerlIO_func struct got shifted or you are using parts of multiple, incompatible versions of Perl so that an attempt to call the function held in the PerlIO_func.Seek slot actually ends up calling the code that should be pointed at by the PerlIO_func.Read slot.