Have been running 1.6.0 Nov build on Due and just noticed this.
I am reluctant to "upgrade" to 1.6.3 "just because" since 1.6.0 works for me so far.
I can hack this problem by duplicating the last printf lines but would like to know what COULD be the real cause of this.

Here is a simple test of printf and its output
The problem is - LAST printf is always missing from monitor output.

1. Number of for iterations makes no difference
2. monitor baud rate makes no difference
3. removing the "count blank " line will make the previous for loop miss the past printf.

# define DEBUG
void setup() {
 // put your setup code here, to run once:
 //Serial.begin(115200);
 Serial.begin(9600); 
 delay(1000);
 for (int i = 0; i <= 5; i++)
 printf("\n Count %i ", i);
# ifdef DEBUG
 for (int i = 0; i <= 5; i++)
 printf("\n Count %i ", i);
# endif
 for (int i = 0; i <= 5; i++)
 printf("\n Count %i ", i);
 printf("\n Count blank "); // missing from output 
}

Sample code

 Count 0 
 Count 1 
 Count 2 
 Count 3 
 Count 4 
 Count 5 
 Count 0 
 Count 1 
 Count 2 
 Count 3 
 Count 4 
 Count 5 
 Count 0 
 Count 1 
 Count 2 
 Count 3 
 Count 4 
 Count 5