The differences just have to do with different software.  The card starts with certain defaults defined in the BIOS - "something" is changing them after you get started up.

If you've got a third party card and install third party tools (MSI AfterBurner, for example) then that will most certainly have a different "default" than Catalyst 11.5 on Linux.  There is also chance you're also using a branded driver - Dell, Lenovo, etc will supply a Catalyst driver that is "tailored" to their computers rather than the vanilla Catalyst driver.

Catalyst 11.5 and Catalyst 11.6 under Linux even sometimes show different values on some cards.

The 69xx series cards are some of the newest cards with totally different architectures.  I've had some issues with 6950 and 6970 series all over the board - one of my 6950s didn't even have a working fan control in Linux.  Setting it to "auto" wouldn't start the fan until the card was over 85C.... which is far too late to start trying to cool it....

AMD/ATI's drivers in Linux have always sucked.  Always.  Realistically, their drivers aren't much higher quality in Windows, either.

Make sure you're using Catalyst 11.6 and SDK 2.4 with the 69xx series.