My level 4 3 checks run was retimed as 2seconds. The starting time was 10minutes and i had 9minutes 59 seconds when i finished the run. Should the time not be 1 second instead of 2

Ending it at 10 minutes and 0 seconds would be 1 second as that is rounded up from 0.x seconds. We are not able to record runs as 0 seconds, so rounding up to the next whole second is the best thing we can do.

If that is the case then alot of the 1 second runs on the board would be 2 seconds

You are correct. I need to go through and fix all the mistakes the past moderator let slip by. Thank you!