We don't know. In the first season of Heroes, there was never any indication that the viewers had seen all of Sylar's powers. It was consistently a mystery how many people he had killed and taken abilities from. The fact that he could manifest new powers at any time was part of what made him such a tremendous potential threat.
However, from an out-of-universe perspective, there was a reason that this scene was put in. The original conception of the Heroes franchise was that each season/volume would feature a new group of characters, learning about their powers and dealing with fresh threats (with possible cameos by characters from earlier volumes). This was an unusual idea, and I think it would have worked. However, when the first season of the show was a significant success, and some of the characters became quite popular, NBC wanted to do away with the original plan and keep the same popular characters around for subsequent seasons.
This might have been workable, but the new setup presented one very obvious problem. Several of the characters had become far too powerful and proficient in the use of their powers: Peter, Hiro, and Sylar, in particular. Various methods had to be taken in subsequent seasons to "nerf" these Peter's and Hiro's abilities, so they could not solve all of a new season's problems in just a few minutes. Peter spent most of the second season with amnesia, keeping him for being effective. Then he was reduced to having only one power at a time, rather than all he had accrued, which reduced his power to a manageable level.
Hiro's powers were "nerfed" in a piecemeal fashion. First, he spent much of season 2 in medieval Japan, and after that, various other devices were used to limit the effectiveness of this abilities. At one point, he was regressed to a childlike mentality. Another element introduced was characters who were able to overcome Hiro's time-stopping ability. The most notable character with this ability was the speedster Daphne, who moved at normal speed even when time was supposedly stopped. (That this could actually stymie Hiro really made no sense, since Hiro could also reverse time, but the producers seem to have hoped that the viewers would simply have forgotten about that.)
Sylar being able to shake off the effects of the stopped time was just an early example to show that Hiro's temporal powers did not make him all-powerful. It was there to demonstrate that the villain was still a threat, even when there was a protagonist with control over space and time.