Easy solution to the problem - Don't use AUTO anything! When I shoot flash, I usually go into Manual mode, set the ISO to 400, shutter speed to 1/125, and then the aperture to whatever DOF I want (usually keep it around f/4.5 though). This way the only thing the camera decides is how much flash power to use. And it's usually pretty accurate.
If I'm in a big room/high ceiling, I might go to ISO800. If the background needs more exposure, I might lower the shutter speed to 1/100 or so.
If you want to get the best out of your camera, don't let it set stuff for you. :-)
When I go flash-less, I just go into Av mode and alway keep an eye on the shutter speed. If it gets to be too slow for the aperture I want, I boost the ISO.
I hit the limit of my f/2.8 zoom this weekend. In our basement at night, just regular tungsten lighting. I was (well the lens was) wide open (f/2.8), ISO3200, and I still could only get away with 1/80s or so. I was using my flash but the batteries died
I should have grabbed by 50mm f/1.4, then I could have backed down to ISO800 :-) (I love using that lens wide open!)