I did it in basic shell script with nanoseconds:
while read line
do
d1=$(echo $line | cut -d, -f1)
d2=$(echo $line | cut -d, -f2)
ds1=$(date -d"$d1" "+%s.%N")
ds2=$(date -d"$d2" "+%s.%N")
diff=$(echo "$ds2 - $ds1" | bc)
printf "$ds2 - $ds1 = %.3f\n" $diff
done < file
Test
$ while read line; do d1=$(echo $line | cut -d, -f1); d2=$(echo $line | cut -d, -f2); ds1=$(date -d"$d1" "+%s.%N"); ds2=$(date -d"$d2" "+%s.%N"); diff=$(echo "$ds2 - $ds1" | bc); printf "$ds2 - $ds1 = %.3f\n" $diff; done < file
1373524748.748000000 - 1373524748.748000000 = 0.000
1373524748.826000000 - 1373524748.826000000 = 0.000
1373524748.860000000 - 1373524748.860000000 = 0.000
1373524748.919000000 - 1373524748.919000000 = 0.000
1373524748.941000000 - 1373524748.941000000 = 0.000
1373524749.390000000 - 1373524749.390000000 = 0.000
1373524749.594000000 - 1373524749.594000000 = 0.000
1373524749.619000000 - 1373524749.619000000 = 0.000
1373524749.787000000 - 1373524749.787000000 = 0.000
1373524750.006000000 - 1373524750.006000000 = 0.000
1373524750.017000000 - 1373524750.017000000 = 0.000
1373524750.088000000 - 1373524750.088000000 = 0.000
1373524750.214000000 - 1373524750.214000000 = 0.000