I might be having a similar problem.
I have 2 drives in a new USB 3.0 dock. One of the drives has two partitions, the other one has one partition.
With the two partition drive in particular, I have one partition as a time machine backup. Often (but not always), when I go away for an extended period of time, Time Machine reports that it couldn't backup because it can't create a directory.
Looks like the drive was ejected. I get the message, "disk was improperly ejected".
I have the laptop set to never sleep.
For a while I thought it was the option to let the drives spin down. If I set that off, it seemed to fix the problem. But sometimes even with it set on, and the drive spun down, it works fine.
I've been off on a tangent thinking maybe the drive was overheating in the dock. I had the other drive eject as well even though it has one partition.
I put them back in their previous USB 2.0 case. I discovered using S.M.A.R.T. that the drives run even hotter there so that's likely not the cause of the problem.
So now I'm down to thinking its either a USB 3.0 issue with the Macbook Air or with Mountain Lion, or an issue with the USB 3.0 dock.
I also had a situation where USB communication suddenly stopped. The Macbook was still running, but if I ever asked any app to do anything with the file system, it would hang. Eventually the whole machine was hung and I had to hard power off.