Why is printing "B" dramatically slower than printing "#"?

Pure speculation is that you're using a terminal that attempts to do word-wrapping rather than character-wrapping, and treats B as a word character but # as a non-word character. So when it reaches the end of a line and searches for a place to break the line, it sees a # almost immediately and happily breaks there; whereas with the B, it has to keep searching for longer, and may have more text to wrap (which may be expensive on some terminals, e.g., outputting backspaces, then outputting spaces to overwrite the letters being wrapped).

But that's pure speculation.

I performed tests on Eclipse vs Netbeans 8.0.2, both with Java version 1.8; I used System.nanoTime() for measurements.

Eclipse:

I got the same time on both cases - around 1.564 seconds.

Netbeans:

Using "#": 1.536 seconds

Using "B": 44.164 seconds

So, it looks like Netbeans has bad performance on print to console.

After more research I realized that the problem is line-wrapping of the max buffer of Netbeans (it's not restricted to System.out.println command), demonstrated by this code:

for (int i = 0; i < 1000; i++) {
    long t1 = System.nanoTime();
    System.out.print("BBB......BBB"); \\<-contain 1000 "B"
    long t2 = System.nanoTime();
    System.out.println(t2-t1);
    System.out.println("");
}

The time results are less then 1 millisecond every iteration except every fifth iteration, when the time result is around 225 millisecond. Something like (in nanoseconds):

BBB...31744
BBB...31744
BBB...31744
BBB...31744
BBB...226365807
BBB...31744
BBB...31744
BBB...31744
BBB...31744
BBB...226365807
.
.
.

And so on..

Summary:

Eclipse works perfectly with "B" Netbeans has a line-wrapping problem that can be solved (because the problem does not occur in eclipse)(without adding space after B ("B ")).

Yes the culprit is definitely word-wrapping. When I tested your two programs, NetBeans IDE 8.2 gave me the following result.

First Matrix: O and # = 6.03 seconds Second Matrix: O and B = 50.97 seconds

Looking at your code closely you have used a line break at the end of first loop. But you didn't use any line break in second loop. So you are going to print a word with 1000 characters in the second loop. That causes a word-wrapping problem. If we use a non-word character " " after B, it takes only 5.35 seconds to compile the program. And If we use a line break in the second loop after passing 100 values or 50 values, it takes only 8.56 seconds and 7.05 seconds respectively.

Random r = new Random();
for (int i = 0; i < 1000; i++) {
    for (int j = 0; j < 1000; j++) {
        if(r.nextInt(4) == 0) {
            System.out.print("O");
        } else {
            System.out.print("B");
        }
        if(j%100==0){               //Adding a line break in second loop      
            System.out.println();
        }                    
    }
    System.out.println("");                
}

Another advice is that to change settings of NetBeans IDE. First of all, go to NetBeans Tools and click Options. After that click Editor and go to Formatting tab. Then select Anywhere in Line Wrap Option. It will take almost 6.24% less time to compile the program.

https://i.stack.imgur.com/yv2eL.jpg