I'm only using a Kit lens ... 18-55 on my 350D ... I rarely uses the built-in flash so I never had that problem, if I can't focus, i just give a quite flick and turn off the AF and switch to Manual focus... it's easy mah...
I supposed you're using a Nikon which in a way, has problems in low light conditions. If crank up the ISO, problem with NOISE will appear... but if you can, go invest in the upcoming D300 or the D3 ... beautiful with barely visible noise even at ISO3200