Hi Stacy,
I struggled with my pup's weight until very recently (he's just now 8 months). At 4 months he still only weight 25lbs (he was the runt, though, so only 12lbs at 9 weeks). By 4 months he was eating 6 cups of dry biscuit a day by 4 months (now he's at 8). He's 80lbs and still has that really skinny look but looks less scrawny. He's got a fast metabolism. He eats far more than my friend's Mastiff puppy at roughly the same age. I worried for a couple months (my graduate work is in animal nutrition so I knew he was getting great nutrition through his food) and was considering having the vet run tests. I gave it a couple months and he's starting to look 'right' finally.
Gummy Bear, my boy, also has a terrible stomach. If you could feed him four times a day it'll help the stress on his digestive system. Regarding food, you may have to experiment with carbs and proteins. Gummy doesn't do well with rice, but he does very well with lentils and potatoes. He seems to do better with duck and fish than he does with chicken (red meats are completely out of the questions). You can try pumpkin, yoghurt and other sources of probiotics if the supplements aren't working. Adding dry food probably won't help much (and if you do, avoid anything with by-products and corn as these are fillers. Avoiding soya is also advisable as well as wheat if he has a sensative stomach). NOrmally when dogs have digestive problems adding raw foods is the answer not kibble. That being said, he may be getting too much protein or too much carbs. Be careful to ensure the protein/fat/carb/calcium/phosphorous amounts are right for his breed. You want to keep him from growing too quickly to fast. You want low carb/low fat (the fat could also be causing his stomach problems).
It can take quite a while to sort out upset stomachs. Just keep working on it. You can also ask the vet to test for giardia (possibly he drank from a puddle or lake/river).
Cheers,