My daughter has a 300d ,and when using the built in flash all the pictures are way overexposed.With another flash they are okay.It does not matter what the camera is set at automatic or any other setting.I use all nikon equipment have not been able to figure it out.With the auxilary flash I just compensate for it but I can't do it with the on board flash.
I"ve had similar issues with my d.reb. I've found that it just doesn't work very well with the onboard flash. Once you put an external flash on, it works like a charm. I don't really know of any way to fix it other than getting an external flash.
You can also do the Wasia hack on the camera and one of the things that will do is let you turn the flash exposure up or down by a few stops. Works with on board or hotshoe flash. When I had my DReb I used that with a Sigma 500 DG and got very consistant exposure with no overexposure problems.