When I change the setting of some applications in xp pro(like winrar , startup list ,Google preferences etc), they come back to their previous configuration when I reboot.
I have tried many things:
1)updating windows
2)scanning for viruses with nod32 , scanning for Trojan horses with tauscan,checking for spywares with ad-aware , spyware doctor , antispyware
3)defragmenting disk with perfectdisk , cleaning registry with cleanmypc and registry mechanic , optimizing my xp with advanced system optimizer .
Nothing helped.
I also noticed that some registry keys came back to the registry after reboot , although I had cleaned them with some registry cleaners.
Please help.

I would suggest that you uninstall and ditch all the optimisation programs and utilities that you have, with the exception of NOD32 and AdAware. Add Spybot Search & destry to your collection, then thouroughly scan your system again, (from 'Safe Mode') with each of those tools, making sure that they are the latest versions and have their definition files updated first.

The perform an in-place upgrade of Windows:

http://support.microsoft.com/default...&Product=winxp

If your system still behaves oddly, consider a format and fresh install of Windows and your programs, this time avoiding all those gimmicky tools which claim to look after your PC for you. When you use a battery of those, all you ever end up doing is creating another mess to replace the one you had.