I've had this issue in the past and someone over at GetDPI just posted with the same problem. Since there are more Phase folk here, I thought I'd cross post in case anyone knows a solution.
If you are shooting straight up or straight down and have the camera doesn't know which way is up (the gyro can't find vertical) then when the images come into a tethered session, C1 Pro doesn't know which way to orient them.
So, then I just use the rotation tool to put the proper end up and apply whatever crop and other adjustments I want. The problem is that when the next capture comes in (from the same setup), C1P will apply all the settings from the previous capture EXCEPT the rotation. So, I have to manually rotate (and re-crop) every capture that comes in.
What gives?