fill problem

Can you select the Layer item in the Appearance panel and select "Clear Appearance" from the Appearance panel menu?

Your description of your process doesn't really make it clear what you're doing, what result you expect, and what unexpected result you're getting. Will you please try the below and report back?

1. Create a new document to work in. Choose File > New, and select any of the presets on the Web tab.
2. Before you draw anything at all, press the D key on your keyboard.
3. On the Tools panel, select the Rectangle Tool and draw a rectangle. It will have a white fill and black stroke, unless something is wrong in Illustrator.

If that works as planned but doesn't in another document, try this:

1. Choose Window > Graphic Styles to open that panel.
2. Choose Select > Deselect. If it's greyed out, that's okay.
3. Activate the Zoom tool on the Tools panel by clicking on it (don't use a keyboard shortcut).
4. Look at the Graphic Styles panel. Is there a thin rectangle around any of them, indicating that they're selected?
5. If so, click the very first graphic style, the Default, with white fill, black stroke.
6. Try drawing a new object and see if it fills white, strokes black, or something else; then try to change the fill to your pattern fill.

How do you create your fills?

Can you perhaps show a screenshot that includes the selected object and the Appearance panel (From Window > Appearance)