I'm sure a PCI-E 2.0 Graphics card will function find in PCI-E 1.1 Slots, I mean the PCI-E freq or 2.0 is 175mhz Vs 100mhz of 1.1 right? if so you can overclock PCI-E freq on most mobos.
The cards auto negotiate withe the controller to determine the link width and speed so there would be no need to overclock the PCI-E frequency.
Remember the changes from AGP x1 , x2, x4, x8
The only point at which card became incompatable was when the voltage changes from 3.3v to 1.5v and even then for a period mainboards supported both options.
Current PCI-E cards don't need the PCI-E 2.0 bandwidth so the only reason they'd move to the standard is if it was compatible with previous generations. The transition from AGP to PCI-E took a fair bit of time in 'component lifecycles'
I'm sure it will work just fine.
AD
Edit,
This seems to be the source of the issue:
http://www.beyond3d.com/content/news/421
Seems limited to a single SKU with a cross switch, seeing as it was written near 2 months ago there would be a lot more info about if it was a major problem
Other info
http://www.electronicsweekly.com/Articles/2007/08/20/42040/pci+express+prompts+quiet+evolution.htm
http://www.xbitlabs.com/news/mainboards/display/20070817093804.html
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