I'm in a similar situation with my DS. He's 13 1/2 months old and has been on Enfamil Nutramigen full time since he was around 9 months old, for both his eczema and problems with gas. When he turned a year old his pediatrician recommended that we switch him to regular formula to see what would happen before switching him to whole milk. The first time we tried regular formula when he was 9 months old, he would get a red rash all over his face and body. Well, this time, there was no rash, but he developed terrible gas and would wake at night screaming. When I would go in to him he would burp when I picked him up and then fall back asleep. After three days of this, I put him back on the Nutramigen and he was fine, no gas. I've also tried doing a mix of 1/4 lactose free formula in with his Nutramigen thinking that he could possibly be lactose intolerent and I could introduce the lactose free formula gradually. Again, he woke up at night with gas pain. So we're back again on the Nutramigen (and going broke during the process!)
We had three blissful weeks of him quickly going to sleep and then sleeping through the night for the first time in his entire life. These formula trials are messing with that bliss!!!
So I'm here to commiserate with you and I hope someone can help us both!