Difference in results when running the different version but simple script.

I make my own script about calculating the transition probability of Markov Chain.I run the two scripts and get different results.Can you detect what makes the difference? What I was doing is

 [t,j]=size(sets);

 p00=zeros(j,1);
 p01=zeros(j,1);
 p10=zeros(j,1);
 p11=zeros(j,1);

 for i=1:j,
    prev=sets(1:t-1,i); 
    next=sets(2:t,i);

    p00(i)=sum(prev <= 1 & next <= 1)/sum(sets<=1);
    p01(i)=sum(prev <= 1 & next > 1)/sum(sets<=1);
    p10(i)=sum(prev > 1 & next <= 1)/sum(sets>1);
    p11(i)=sum(prev > 1 & next > 1)/sum(sets>1);
  end

Another very similiar version is

for i=1:nv,
  s0=sequence(1:nt-1,i);
  s1=sequence(2:nt,i);
  ndry=length(find(s0 <= threshold));
  nwet=length(find(s0 > threshold));
  p00(i)=length(find(s0 <= threshold & s1 <= threshold))/ndry;
  p01(i)=length(find(s0 <= threshold & s1 > threshold))/ndry;
  p10(i)=length(find(s0 > threshold & s1 <= threshold))/nwet;
  p11(i)=length(find(s0 > threshold & s1 > threshold))/nwet;
end