There is nothing wrong with backing up any and all system files that you wish, in your user's home folder. HOWEVER, please note what happens to the ownership when the user makes the backup:
Code:
don@imerabox:~$ ls -la /etc/sysctl.conf
-rw-r--r-- 1 root root 2246 Nov 3 2011 /etc/sysctl.conf
don@imerabox:~$ cp /etc/sysctl.conf .
don@imerabox:~$ ls -la sysctl.conf
-rw-r--r-- 1 don don 2246 May 4 15:45 sysctl.conf
Any file copied by the user into his home directory becomes his file. What you have apparently done is used "sudo" or a root-mode file manager and copied system files into your user's folder -- that is a no-no. Moreover, you have somehow managed to create configuration files of such tools as aptitude in the user's home folder, with root ownership. For example, to run a KDE user session, everything under ~/.kde has to be owned by the user:
Code:
don@imerabox:~$ ls -la .kde
total 32
drwxr-xr-x 6 don don 4096 Nov 21 13:08 .
drwx------ 54 don don 12288 May 4 15:45 ..
drwxr-xr-x 2 don don 4096 Apr 28 15:14 Autostart
lrwxrwxrwx 1 don don 21 Nov 15 09:04 cache-imerabox -> /var/tmp/kdecache-don
drwxr-xr-x 2 don don 4096 Nov 21 13:08 env
drwxr-xr-x 6 don don 4096 Nov 21 13:08 share
drwxr-xr-x 2 don don 4096 Nov 21 13:08 shutdown
lrwxrwxrwx 1 don don 16 Nov 15 09:04 socket-imerabox -> /tmp/ksocket-don
lrwxrwxrwx 1 don don 12 Nov 15 09:04 tmp-imerabox -> /tmp/kde-don
I'm not willing to spend any more time debating it -- we have found the cause of your broken KDE login.