Gradient tool doesn't fill repeatedly

What you describe certainly sounds like the default behavior of the Gradient tool. There are settings that can be changed which can result in different behaviors which may be more in line with your expectations and likely you had enabled previously but they were reset back to default. 

The first to look at is whether you were previously using the new Gradent tool or the Classic gradient tool. The new one has the on-canvas widget which allows you to dynamically create and modify your gradient with on screen controls. The Classic just lays the pixels on the canvas with no way to change it once it's been created. 

Second, is your gradient using transparency? If not, any time you redraw your gradient it will lay down fresh pixels which will completely cover what you had before. If you use transparency though, the transparent parts of the gradient will allow the under portions of previous gradients to show through.

Third, similar to transparency, if you are working with Classic gradient, you can change the Blend Mode (the Mode drop-down). This causes the gradient you apply to compare it's pixels to those which are already present and change their behavior based different characteristics. This could allow you to build up a look through multiple applications. 

Hopefully one of these is what you are looking for.