are you sure you're changing the FPS in the timeline? The two number boxes on the left and right of the time line represent min/max frames and specify what range of frames are displayed in the timeline.

So, for example, if you have 500 max frames, and you tell it to display all 500 frames, but then change the number of max frames to, say, 100, then the max display number will also change to reflect that it no longer has 500 frames to display... just the 100 you changed it to.