What does Java do with the input file?

Hello everyone --
I have a freaky Java problem. I'm running a program that takes an input file, reads it one line at a time, and determines whether the info I'm looking for is contained in it or not. For each line it reads, it decides if that line is good or bad, and broadcasts the findings in a System.out.println(). Every line gets one. When I run the program, I redirect the output to a log file. What's going on when the input file is 13000+ lines long and the log file is only 2500 lines long? This is tweakin' me out.
Thanks for the advice,
-Kwj.

Here's what I have:
boolean isGood = true;
int count = 1;
while((line = in.readLine()) != null)
if (/*some condition is met*/)
{*do some stuff*/}
else
isGood = false;
System.out.println("***" + line);
if (isGood)
/*do some more stuff*/
System.out.println(count + ". " + line)
count++;
}//process all lines
As far as I can tell, I have every line accounted for in the else statement or the last if statement. If the line doesn't meet the req., it doesn't get to go on to the last if processing. All the good ones get processed. I think.

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