It could be the squirrels or birds. Birds (especially crows) often take new young growth to feed to their young. Perhaps you should invest in bird netting or row cover material to protect your new seedlings until they are tougher. At that point, they are seldom bothered.
Also, check your fencing to make sure that it is partially below soil level. Rabbits will crawl under any fence that has an opening at the base.
The damage could also be caused by insects. Go out periodically (after dark as well) and check to see if anything is munching on your plants.
The first step, of course, is to identify the culprit. The resources at the Internet Center for Wildlife Damage Management (Identifying Animal Damage) should help.
