I think a milk allergy is a strong possibility. If it is a bit better with the mixture of the soy that could be your answer. I think to know for sure he will have to be completely off the regualr formula for a bit and if the improvement is better or he stops completely you have your answer. The rabbit is a possibility, but the question is does he get worse when he goes to your mother's? If he does and then improves after a day or 2 at home you may need to have grandma come see him at your house and not go to hers. You should wait to see how he does when he is completely on the soy. If after a while there is no improvement start keeping a log of when he gets more congested,(where has he been, what has he been around, how long he was around it, how long it takes him to improve etc), that way you may be able to figure out what triggers his symptoms. Then you and your doctor can figure out what you need to do to solve the problem. I would try not to worry to much unless it is really affecting his ability to sleep. It may staighten itself out on it's own. Try not to stress yourself out over it. If he is otherwise healthy, try to keep telling yourself you will find the answer in time. You are not a new mother so you know when something isn't right, trust your instincts. If you aren't getting any improvement and the doctor still insists it's nothing to worry about try another doctor and then another until you get an answer that makes sense. I know how hard it is. Last summer my DS came down with what seemed like a stomach virus, but he would be really sick to his stomach for a day and then feel better the next, he'd have a high fever for a day or so and it would go down and come back up. After a week of this I took him in to be told he just has a virus. The next day he developed a rash. I took him back in and the doctor treated me like a hysterical mother (I've been at this 10 years and I am most definitely not that), looked at the rash and said yeah he has one but I don't know why(this was a DR who was normally at a different office) and sent me home again. The next day he had his highest temperature yet and was very lathargic so I took him into the ER. I just knew this was more then a virus. We got really lucky and got a doctor who looked at his rash(by now the small spots were huge and red with a white center) and listened to his symptoms and said, "He has Lyme Disease." This made sense to me as he had been up at my IL's cabin 2 weeks before in northern Minnesota. He brought in another doctor who insisted it was a viral rash and every nurse in the place came to see the rash for themselves because no one had ever seen Lyme. They did a spinal tap and ran all kinds of test. We went home on amoxicillan, and back to our regular doctor the next day. He was so much better after 12 hours on the antibiotic I was convinced he did infact have Lyme. Our doctor who I trust implicitly still wasn't convinced, but a week later the initial test indicated he did have it. We had to wait for the Mayo Clinc to give us the definitive answer a week later, but I am glad I stuck with it because he could have had some serious permanent side effects if they had taken longer to get the right diagnosis. I am not saying you are dealing with anything this life altering because I am sure you aren't. I am only telling you this so you stick with it if you are really sure there is something going on and don't let the doctors poo-poo you into thinking you are overreacting. Good luck. I hope the soy formula solves your problem.
take a nice shower with the baby. We did this all the time. they hardly ever took a bath. Loved being held in the shower. Warm water and steam. 
