I went through this as well. I missed the fact that "seconds" is not how many seconds it took you from reset to continue. It's literally "seconds" as in time, time on the DS clock. So if you reset at 12:00, and hit "continue" at 12:00 and 15 seconds, the seconds should be 15. If you reset at 12:00, 30 seconds, and hit "continue" at 12:00 and 45 seconds, your "seconds" will be 45. I hope this explains it.
Perhaps this part of the RNG article could be improved to reinforce the fact that "seconds" is not just delay in a different unit of measurement.