Today, I played 'Indy and The Infernal Machine' from scratch at Canyonlands level in my PC and posted a time of 0:05 (checked at Games Statistics) for the final end of the level before Indy meets Sophia. However, in a saved file which I played in 2001, at the same end of the level, I checked that I posted a time of 0:00. How is this possible?

That time is actually from your last quicksave, not from the beginning of the game. You probably quicksaved just before you did that last big jump, as most gamers would.

woodenstool,
1) File is not 'Quicksaved'; it a file with specific name that I saved
2) The game was played in 2001 from the beginning though I may have saved using a combination of named files and 'quicksaves'.
3) Other files at the final end of other levels that I saved (not quicksaved) eg. Shambala Sanctuary recorded a total time of 0:18. This Shambala file 'continues' from the Canyonlands file.

Many 'glitches' were found in "Infernal Machine" your timing might be one of them.