EDIT:

And why doesnt it work in this code, grep couldnt find any non-ascii symbols in this file:

import java.util.ArrayList;
import java.util.Iterator;
import java.util.Scanner;
import java.util.Collections;
import java.util.regex.Pattern;
import java.util.Arrays;
import java.io.*;
public class DFK {
 static ArrayList<Path> done = new ArrayList<Path>();
 public static void print() {
 for(Path i: done) {
 //System.out.println(i+" "+i.isConverted());
 if(i.isConverted()) {
 System.out.println(i.getConverted());
 }
 }
 }
 public static void develop() {
 if(done.get(0).getKP1() > 0) {
 DFK.add(new Path(done.get(0).getP(), done.get(0).getQ(), done.get(0).getK()));
 DFK.add(new Path(done.get(0).getP(), done.get(0).getKP1(), done.get(0).getK()));
 DFK.add(new Path(done.get(0).getKP1(), done.get(0).getKP1(), done.get(0).getK()));
 DFK.add(new Path(done.get(0).getKP1(), done.get(0).getQ(), done.get(0).getK()));
 }
 }
 public static void add(Path x) {
 boolean exists = (done.indexOf(x)==-1 ? false : true);
 if(exists == false) {
 done.add(x);
 if(x.getKP1() >= 2) {
 DFK.add(new Path(x.getP(), x.getQ(), x.getK()));
 DFK.add(new Path(x.getP(), x.getKP1(), x.getK()));
 DFK.add(new Path(x.getKP1(), x.getKP1(), x.getK()));
 DFK.add(new Path(x.getKP1(), x.getQ(), x.getK()));
 }
 }
 }
 public static void main(String argv[]) throws IOException {
 BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
 int p = 0, q = 0, kp1 = 0;
 Scanner in = new Scanner(System.in);
 System.out.print("p = ");p = in.nextInt();
 System.out.print("q = ");q = in.nextInt();
 System.out.print("k+1 = ");kp1 = in.nextInt();
 System.out.print("\n");
 String rkzero[][] = new String[q][q];
 for(int i=0; i<q ; i++) {
 for(int j=0; j<q ; j++) {
 System.out.print(String.format("r(%d,%d,0): ", i+1, j+1));
 rkzero[i][j]=input.readLine();
 }
 }
 done.add(new Path(p, q, kp1));
 DFK.develop();
 Collections.sort(done);
 for(int z=0; z<q ; z++) {
 for(int j=0; j<q ; j++) {
 for(Path i: done) {
 String reg = String.format("r(%d,%d,0)",z+1,j+1);
 i.setConverted(i.toString().replace( reg , rkzero[z][j])); //HERE IS THE PROBLEM
 }
 }
 }
 System.out.print("\n");
 DFK.print();
 }
}
class Path implements Comparable<Path> {
 int p,q,kplus1,k;
 String converted = null;
 public int getP() {
 return p;
 }
 public int getQ() {
 return q;
 }
 public int getKP1() {
 return kplus1;
 }
 public int getK() {
 return k;
 }
 public Path(int a, int b, int c) {
 super();
 p = a;
 q = b;
 kplus1 = c;
 k = c-1;
 }
 public boolean equals(Object obj) {
 if (obj == null) {
 return false;
 }
 if (!Path.class.isAssignableFrom(obj.getClass())) {
 return false;
 }
 final Path other = (Path) obj;
 if(other.p == this.p && other.q == this.q && other.kplus1 == this.kplus1)
 return true;
 return false;
 }
 public int compareTo(Path other) {
 return other.kplus1-kplus1;
 }
 public String toString() {
 return String.format("r(%d,%d,%d)=r(%d,%d,%d)+r(%d,%d,%d)r(%d,%d,%d)*r(%d,%d,%d)",p,q,kplus1,p,q,k,p,kplus1,k,kplus1,kplus1,k,kplus1,q,k);
 }
 public void setConverted(String x) {
 converted = new String(x);
 }
 public String getConverted() {
 return converted;
 }
 public boolean isConverted() {
 if(converted == null)
 return false;
 return true;
 }
}

This is the output:

p = 1
q = 2
k+1 = 2
r(1,1,0): 0
r(1,2,0): 1
r(2,1,0): 1
r(2,2,0): 0
r(1,2,2)=r(1,2,1)+r(1,2,1)r(2,2,1)*r(2,2,1)
r(1,2,1)=r(1,2,0)+r(1,1,0)r(1,1,0)*r(1,2,0)
r(2,2,1)=0+r(2,1,0)r(1,1,0)*r(1,2,0)

It replaces only r(2,2,0) with 0 and nothing else, I replicated previous problem from this, but I can't find any non-asci symbols in this one.