Same problem here, only it
just started with the install of v3.4.0Beta 18.
As soon as I allowed it to install, I received a message that my wallpaper settings had changed. I tried to click the close button on the balloon, but missed and it changed my wall papers - reversed them from my current settings. I then went exploring in DF, and this is what I came up with:
Windows has my monitors set the way
I want them - Monitor on left (attached to primary video card) is designated the primary monitor, and the monitor on the right (attached to second video card that is SLI'd to primary video card) is designated monitor 2, aka Extended monitor. It was the same in DF as well, until beta 18.
Now, DF shows it reversed - left = 2p, right = 1. See attached screenshot (DP being Displayfusion Pro - if you look up my forum username you won't find it, Jon
may remember me

- PM me for details, and I'll gladly provide them)
Here is the Customer Test output:
Customer Test v1.2.1
Windows: Windows7_Server2008R2
Update Mode: Win7
---------------------------------------------
Monitor #1
VideoCard: NVIDIA GeForce GTX 260
Monitor: X213W
Source: \\.\DISPLAY2
Attached: True
Primary: False
Bounds: {X=1680,Y=0,Width=1680,Height=1050}
Primary: Landscape
OutputTech: DVI
SID: 1
SAID-L: 50198
SAID-H: 0
SMIDX: 3
TID: 5243152
TAID-L: 50198
TAID-H: 0
TMIDX: 3
Connector: 0
---------------------------------------------
Monitor #2
VideoCard: NVIDIA GeForce GTX 260
Monitor: X213W
Source: \\.\DISPLAY1
Attached: True
Primary: True
Bounds: {X=0,Y=0,Width=1680,Height=1050}
Primary: Landscape
OutputTech: DVI
SID: 0
SAID-L: 50198
SAID-H: 0
SMIDX: 1
TID: 3146000
TAID-L: 50198
TAID-H: 0
TMIDX: 1
Connector: 2
---------------------------------------------
2011/09/23 21:37:00.92: INFO: BFMonitorEnum:UpdateMonitors: Updating Monitors All: Constructor
I am I.