I'm running Inkscape 0.48 on SuSE Linux 11.4 64 bit.
I wanted to use the pattern fill on an oval object that had to be tilted (rotated a little bit) and I need the pattern to be at 90° to the canvas, not following the orientation of the object.

Here is the normal object with a pattern fill (checkered):


Here it is again, but the object has been rotated and the fill is also rotated:


I don't want the pattern to be rotated, I want it to be straight despite the orientation of the object. Is there any way to do this? I've tried editing the pattern using the node tool as described in the manual but that did not give me the results I wanted.

Also, can you change the default color of the pattern? As you can see, it is black and white. I want it to match the stroke color.

When you have your active there are four "Affect" icons on the extreme right of your tool control bar, one of these (hover to see which one) is to select/deselect the option to transform your patterns with your object. You want to deselect it. This option is global.
As for the fill color, you will have to do "pattern to object'" (object menu, but you could skip this and just draw on the canvas as you would like the new pattern to be), change the fill, then do "object to pattern" and then select the new pattern for your fill.