It is probably just because in different parts in a game, the detail level increases and the processes that the graphics card must process increase as well. Here's an example. When I play Far Cry on my computer, on the menu screen, I get about 200 FPS. However, when I get into the game (actually playing; walking around and shooting things), my FPS will drop to around 60 FPS. It's just the load differs when you're playing a game. It isn't constant and the graphics card must process these things when they occur.
So, this is normal.