After getting my EX1 back from Sony Service Los Angeles to the have Battery Drain fix and FW 1.11 upgrade I have run into this anomaly.
Two Formatted 8 gig SxS Cards Installed

In Camera Mode
Slot Select "A" is selected. Green light as expected
Viewfinder indicated "B"
on Record Slot Select "A" is Red as expected
Shot is recorded on Card "A"

The same variation happens when Slot Select "B" is selected
Slot Select "B" is selected. Green as expected
Viewfinder indicated "A"
on Record Slot Select "B" is Red as expected
Shot is recorded on Card "B"

When the camera is connected to the computer via USB
Two icons appear on the desktop as expected.
Untitled
Untitled 1

The file on "untitled" is the file from SxS card "B"
The file on "untitled 1" is the file from SxS card "A"

In Media Mode
Slot Selected is "A"
Video is the shot recorded on "A"
but the viewfinder indicated "B"

The same variation happens when Slot "B" is selected.

I will be contacting Sony Service Los Angeles on Tuesday.

Am I missing something or did something get messed up during the last service?

Sounds like they may have crossed up the connecters for the slots on the inside of the cam which I think need to be disconnected to replace the board for the Battery drain fix...

Gotta Love Sony!!!

My paint is starting to flake off and I too need the battery drain fix but I am holding off until I at least have a spare EX1 or EX3 as I can not afford the down time nor the troubles that may pop up when the camera returns.