"It's like the underwriter looked at the origional loan package and stopped looking as soon as they found a problem. "
That is exactly what they do. This is a commonly known phenomena and should be expected. When working a file if they come across something that is missing they will completely stop, put it aside and work on something else that is complete. When they have a stack of files on their desk, they are not going to piece together something that is not ready. There is no reason they would continue on through the whole thing, wasting their time when they already know it cannot be approved as submitted. This is why a loan officer needs to know exactly what will be required and anticipate what might be required. It's really not that hard to get it all the first time. Unless the u/w is asking for something completely outside the box, it's 100% on the LO to know the guidelines.