sure that warning it's not very nice... :) however I also saw similar difference (about 15%) by running separately the routines and checking with the ps - process status - command.
As I said, I've tried to use Benchmark for the first time (there's always a first time...) for this test. However, I guess it's not a problem of file size that warning.
I'd appreciate, for my learning, if the code would be changed by someone to something that can be bechmarked (if it is not a problem of input file size).