I had that problem when I first brought Lilly home. I discovered that she doesn't like the metal bowls regardless of if she's got her collar (with tags) on or not. I have to use the plastic bowls. Her water bowl is a large bowl while her food bowl is smaller.
I feed both my dogs in their prospective "dens" (RJ's being a crate and Lilly's being her playpen) and I leave their food bowls with them for 15 minutes. Whatever they haven't eaten gets picked up and offered to them the following meal. Lilly hasn't had a problem eating all her food since the first week of bringing her home. I feed twice a day at the same time every day. Lilly is good about letting me know when it's time to eat
