error checking using fsck always gives a strict warning
 

my ubuntu OS is not running well after loading.the timer keeps coming and flickers all the time. i cannot move to my home directory niether i can shutdown coz of the flickering of the timer all the time as if some process is still loading but this thing never stops to happen.moreover the look of my desktop has also changed to something like the default ubuntu desktop look.i think there is some disk error coz earlier i was warned by the os for disk checks but i skipped and now things have become worse however when i try to check for disk errors using sudo fsck -As i always get a strict warning from the os "filesystem /dev/sda is still mounted if you continue u will cause severe file system damage" what should i do should i continue or if there's any other way plzz tell.

Checking a mounted partion can (read will) cause data loss. See if you can unmount the partition.
Else execute 'shutdown -r -F' as root. This will cause the system to reboot and there will be a file system check on the reboot.
Hope this helps.

ok..system rebooted,file checks were performed sucessfully and no errors were found but the file manager is not starting properly on the destop it shows starting file manager and the icon keeps filckering seems like file manager is not executing properly.is there a way i can disable this execution of file manager on startup besides what's this file manager my os is ubuntu 10.04.

how do i backup the system generated file and what use does it make on backing up

Here is an idea. Create a new user with "adduser <username>. This will create an entirely new (and perhaps the correct configuration files for the desktop) profile for the user. And when you log in and then configuration files are good then you should be all good.
Well as far as the backup goes that is my signature. Something that I learned out of experience. I keep backups of /etc /lib /bin and their counterparts in /usr/local so that in case the machine goes down (because of something I did) then there is a backup I can always back up from.
Hope this helps