How dark or light it is outside of Gregory House all depends on Gregory’s mood. Despite his appearance, he’s never actually happy on this inside, thus it stays dark during most of the series.
This is why it appears to be twilight during The Bloody Karte. Gregory is (supposedly) injured, but however this makes up an excuse to be away from Gregory Mama. He was away from Gregory Mama during The Last Train, but it is seen when the main conflict in the season turns up that he still feels guilt for not having any excuse other than wanting to “take a vacation”. This renders this season particularly night-like, even though Gregory seems at his happiest in the first few episodes.
I haven’t watched it in a little while, though, so I could be wrong. I thought I’d just share with you guys my thoughts on it.