Instead of worrying about the small difference between both methods, I'd worry about the tiny throughput you have. Writing the numbers 1 to 100 each on their own line takes 292 bytes. You do 3.51 times a second. Which means you're writing about 1kb/sec.

I'd focus on finding out why you can write only 1kb/sec instead of worrying about the 8% difference in speed. For the recond, on my box, 'File1' is much faster than 'File2', but my 'File2' more than 25 times faster than your 'File1':

         Rate File2 File1
File2 93.0/s    --  -68%
File1  294/s  216%    --
[download]

BTW, if I repeat the benchmark, the variation in results is more than the 8% difference you're measuring.