I have experimented with Windows XP Pro X64, Ubuntu 8.10 x64 and Suse 11.1 x64 and the best combination with Gpugrid and cuda is Suse 11.1 by a factor of 2 times.
I have an AMD Athlon(tm) 64 X2 Dual Core Processor 5200+ [Family 15 Model 67 Stepping 2] with 4 gigs of memory and an EVGA GTX 260 video card. Gpugrid and Boinc would fail with computation errors under Ubuntu 8.1 x64. It would run well under Windows XP Pro X64 but any attempt to overclock the video card would either freeze the system or cause computation errors. Still XP Pro x64 would still crank out a Gpugrid result in 10 to 14 hours.
Suse 11.1 x64 running Nvclock 0.8 beta will turn out the same Gpugrid result in 5 to 6 hours with no computation errors.
Here is what I did:
1) Install Suse 11.1 x64 with Gnome desktop.
2) Add the Nvidia repository to the via
Yast
Sofware Repositories
The Nvidia repository url is:
http://download.nvidia.com/opensuse/11.1/
Install the lastest Nvidia driver via Yast rather than use the Nvidia installation script. The Yast version is 180.22.
YOU DO NOT NEED TO INSTALL THE CUDA SDK SOFTWARE FROM NVIDIA.
Cuda support is provided with the driver.
3) Use Yast - Sofware Management to install nvclock-gtk with the graphical interface.
4) Start the Nvclock-gtk program. Turn the fan speed up to maximum. I set the GPU clock to maximum and did not alter the memory clock setting. I set the settings manually when I start up but you can do an automatic setting via a command line in cron.
5) Download and install the x64 Boinc client and manager version 6.4.5 from Seti@home. There is an rpm version but I have not tried it.
6) Use the Boinc manager to connect to www.gpugrid.net and set up an account.
Start computing with Gpugrid and other Boinc projects
Have fun.

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I was not sure how long the calculations should take under Windows XP x64. I tried using cuda and Gpugrid with a Nvidia 8400GS but the calculations took days and slowed the video display to a crawl. The GTX 260 has been a big step forward.

I had also different cards under XP 64 running, only the driver was a problem, every start used 70 MB video ram more. But my cards are not slower running than under Linux or Vista. I changed the operating system because of the bad driver for XP 64 to Vista 64. Maybe your PC was to weak to feed the GPU with all cores working for CPU projects on Boinc. I always disable one CPU by entering 99% for using multiprocessors. This is be found on advanced, preferences, processor usage.
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@ralph:

1.

But a side note: something was wrong with your XP 64 setup

4) Start the Nvclock-gtk program. Turn the fan speed up to maximum. I set the GPU clock to maximum and did not alter the memory clock setting. I set the settings manually when I start up but you can do an automatic setting via a command line in cron.

Ideally, you change the clock speed before starting Boinc to avoid causing a computation error. This was an issue with Windows XP but has not been a problem for me with Suse 11.1. Under Ubuntu 8.10, the nvclock command line program was unable to alter the clocking of the video card.
In Fedora, are you using the nvclock-gtk or nvclock-qt programs or are you using the command line? Nvclock-gtk works for me but if I alter the memory clock instead of the gpu clock, the screen freezes. Try using nvclock-gtk, only alter the gpu speed and then hit change speeds. It should marginally adjust your memory clock as well. For me, the memory clock slows down slightly when the gpu clock is set to maximum. The overall speed is much better.
Results will vary with different video cards and you may or may not be able to overclock your current card beyond a certain level. Experiment with it but you are always better off with stability once you find a formula that works.
Good luck.

No offense taken.
Ubunutu is a great operating system. The only reason that Suse 11.1 is faster for me with Gpugrid is because the nvclock-gtk program is working for me under Suse 11.1 while the command line nvclock program under Ubuntu was not able to overclock my particular video card. Ubuntu is more user friendly. Suse tends to have more up to date drivers. Both work very well.
Suse was my first linux operating system so I am very familiar with it. Ubuntu or Xubuntu work better on some of the less powerful machines that I have installed linux on.

... the nvclock-gtk program is working for me under Suse 11.1 while the command line nvclock program under Ubuntu was not able to overclock my particular video card.

In Fedora, are you using the nvclock-gtk or nvclock-qt programs or are you using the command line? Nvclock-gtk works for me but if I alter the memory clock instead of the gpu clock, the screen freezes.

When I first started using nvclock-gtk with Suse 11.1 and the GTX 260 a message popped up indicating that the overclocking was done via Coolbits and that this was an older method. Even so the program did allow me to change the fan speed and the Gpu clock. The program did misread the Gpu clock speed but both the nvclock-gtk program and the Nvidia Xserver settings indicated a change in speed and this was reflected in my Gpugrid calculation times.
Hopefully later versions of nvclock-gtk will integrate better with the 200 series video cards.

Just one last add on message. You can get more stable overclocking in linux with the Nvidia XServer Settings program. The nvclock_gtk program is the only one that adjusts the fan speed. The Nvidia XServer Settings program allows you to test the best level of overclocking without freezing the system. Once you set the level, it saves it for the next time that you boot up.

Ralph, I'm interested whether you installed the 'libgtk2.0-dev' package before you installed NVclock0.8b4. Because, without it, and the accompanying X11 files, you will not get all the 'coolbits' overclocking options and, on my installation, NVclock also misreported clock speeds without this package installed.

I've been overclocking my GTX 260 on Ubuntu 8.10 64-bit for a while now with no problems. Well, the only minor problem is that clock speeds reset after rebooting, but I can live with that.

Mark