Sitting on a corn flake...

We were having a problem with Vault this week and thanks to our reseller we figured it out pretty quickly. One of my users was having some strange issues with x-references through Vault via Civil 3D. He would set up a few X-refs and then check the drawing into the Vault project.
Then he'd go back in to check it out and the host drawing and the x-ref would both be marked as "Not checked into Vault" by Civil 3D. This had me stumped for about 3 hours. I uninstalled Civil 3D and Vault, then reinstalled both - that didn't fix it. I logged in as myself at his workstation and saw that the problem went away, so I figured it must be a corrupt windows profile. I renamed it then logged in as the user and that still didn't fix it.
Finally, I gave up and called my reseller. Apparently the user had accidentally set his working folder to "My Documents" in Vault Explorer. Even though the Toolspace VE was set to the "C:/Civil 3D Projects" directory, I guess the X-ref panorama was set to "My Documents". Once the Vault Explorer working folder was set to match the Civil 3D Toolspace, all the problems went away.