The IRS has certain conditions that will automatically cause an amended return to be looked at by human eyes. One of your returns may have triggered one of these conditions, and the other one may not have.
There's really nothing you can do but sit back and wait for the IRS to process your second amended return. If they need more information, they'll contact you. You can also call the number on the letter, but you probably won't hear anything other than "we're still looking at it."
