Couple of things could be wrong if the Arduino won't run with a multimeter in series. Firstly, make sure the meter is set to a current-measuring range (Amps). Then, make sure you have the leads in the proper holes for current measurements; many modern meters have a separate positive terminal for current measuing, as a safety feature. Finally, there's usually a fuse inside the meter to protect it against excessive current, and this may be blown.