Comment 9 for bug 104105

Do you use the closed source nvidia drivers? If yes, then the wrong refresh rate is due to nvidias dynamic twinview stuff.

From the nvidia-glx README:
"Q. Why is the refresh rate not reported correctly by utilities that use the
   XRandR X extension (e.g., the GNOME "Screen Resolution Preferences" panel,
   `xrandr -q`, etc)?

A. The XRandR X extension is not presently aware of multiple display devices
   on a single X screen; it only sees the MetaMode bounding box, which may
   contain one or more actual modes. This means that if multiple MetaModes
   have the same bounding box, XRandR will not be able to distinguish between
   them.

   In order to support DynamicTwinView, the NVIDIA X driver must make each
   MetaMode appear to be unique to XRandR. Presently, the NVIDIA X driver
   accomplishes this by using the refresh rate as a unique identifier.

   You can use `nvidia-settings -q RefreshRate` to query the actual refresh
   rate on each display device.

   This behavior can be disabled by setting the X configuration option
   "DynamicTwinView" to FALSE."

Can you try and add
Option "DynamicTwinView" "false"
to your xorg.conf?