Your SB-600 is helping autofocus by providing an AF-assist light. In low light, the D90’s phase-detect AF system has trouble finding enough contrast to measure focus accurately, so it may hunt back and forth. The speedlight projects a red pattern/grid onto the subject, giving the AF sensor clear edges and contrast to detect, which makes focus lock faster and more reliably.

The light is red partly because it’s less visually disturbing in dark conditions than a bright white light or repeated flash bursts.

Your D90 also has a built-in focus-assist lamp that can be enabled in the menu, so you may see similar improvement even without the speedlight. Keep in mind that AF-assist only works within a limited distance, so it won’t help much beyond the lamp’s effective range.