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I have two kernels on my PC (dont ask me why) do my /boot dir loosk like this:

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[root@basia-pc boot]# ls
config@                              symvers-3.8.13.4-desktop-1.mga3.xz
config-3.8.13.4-desktop-1.mga3       symvers-3.8.13-desktop-1.mga3.xz
config-3.8.13-desktop-1.mga3         symvers-3.8.13-desktop586-1.mga3.xz
config-3.8.13-desktop586-1.mga3      System.map@
dracut/                              System.map-3.8.13.4-desktop-1.mga3
grub/                                System.map-3.8.13-desktop-1.mga3
grub2/                               System.map-3.8.13-desktop586-1.mga3
initrd-3.8.13.4-desktop-1.mga3.img   vmlinuz@
initrd-3.8.13-desktop-1.mga3.img     vmlinuz-3.8.13.4-desktop-1.mga3
initrd-3.8.13-desktop586-1.mga3.img  vmlinuz-3.8.13-desktop-1.mga3
initrd-desktop586.img@               vmlinuz-3.8.13-desktop586-1.mga3
initrd-desktop.img@                  vmlinuz-desktop@
initrd.img@                          vmlinuz-desktop586@

I want to set 3.8.13.4-desktop as default using Control Centre. Using graphic interface I check 3.8.13.4-desktop as default but the system still boot by default with 3.8.13-desktop586. Is any possibility to set new kernel as default manually? After that I will remove 3.8.13-desktop586 kernel from system.

Please show the output of

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ls -al /boot

, ls without options is useless.

So You have:

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[basia@basia-pc ~]$ ls -al /boot
razem 48228
drwxr-xr-x  5 root root     4096 lip 10 20:36 ./
drwxr-xr-x 22 root root     4096 lip 10 20:37 ../
lrwxrwxrwx  1 root root       31 lip 10 20:36 config -> config-3.8.13-desktop586-1.mga3
-rw-r--r--  1 root root   145407 lip  4 16:05 config-3.8.13.4-desktop-1.mga3
-rw-r--r--  1 root root   144945 maj 14 21:15 config-3.8.13-desktop-1.mga3
-rw-r--r--  1 root root   144882 maj 14 21:07 config-3.8.13-desktop586-1.mga3
drwxr-xr-x  2 root root     4096 maj  5 20:34 dracut/
drwxr-xr-x  2 root root     4096 cze 16 16:33 grub/
drwxr-xr-x  6 root root     4096 lip 10 21:24 grub2/
-rw-------  1 root root  8902307 lip 10 20:04 initrd-3.8.13.4-desktop-1.mga3.img
-rw-------  1 root root 14382584 cze 16 16:42 initrd-3.8.13-desktop-1.mga3.img
-rw-------  1 root root  8901227 cze 29 14:09 initrd-3.8.13-desktop586-1.mga3.img
lrwxrwxrwx  1 root root       35 cze 29 14:09 initrd-desktop586.img -> initrd-3.8.13-desktop586-1.mga3.img
lrwxrwxrwx  1 root root       34 lip 10 20:04 initrd-desktop.img -> initrd-3.8.13.4-desktop-1.mga3.img
lrwxrwxrwx  1 root root       34 lip 10 20:04 initrd.img -> initrd-3.8.13.4-desktop-1.mga3.img
-rw-r--r--  1 root root   186584 lip  4 16:05 symvers-3.8.13.4-desktop-1.mga3.xz
-rw-r--r--  1 root root   186104 maj 14 21:15 symvers-3.8.13-desktop-1.mga3.xz
-rw-r--r--  1 root root   186264 maj 14 21:07 symvers-3.8.13-desktop586-1.mga3.xz
lrwxrwxrwx  1 root root       35 lip 10 20:10 System.map -> System.map-3.8.13-desktop586-1.mga3
-rw-r--r--  1 root root  2081951 lip  4 16:05 System.map-3.8.13.4-desktop-1.mga3
-rw-r--r--  1 root root  2076466 maj 14 21:15 System.map-3.8.13-desktop-1.mga3
-rw-r--r--  1 root root  2078679 maj 14 21:07 System.map-3.8.13-desktop586-1.mga3
lrwxrwxrwx  1 root root       31 lip 10 20:04 vmlinuz -> vmlinuz-3.8.13.4-desktop-1.mga3
-rw-r--r--  1 root root  3307792 lip  4 16:05 vmlinuz-3.8.13.4-desktop-1.mga3
-rw-r--r--  1 root root  3303424 maj 14 21:15 vmlinuz-3.8.13-desktop-1.mga3
-rw-r--r--  1 root root  3303568 maj 14 21:07 vmlinuz-3.8.13-desktop586-1.mga3
lrwxrwxrwx  1 root root       31 lip 10 20:04 vmlinuz-desktop -> vmlinuz-3.8.13.4-desktop-1.mga3
lrwxrwxrwx  1 root root       32 cze 29 14:09 vmlinuz-desktop586 -> vmlinuz-3.8.13-desktop586-1.mga3

Do you use grub or grub2, and please show the config.

I use grub2. But now I am far from this computer. Will send You config ASAP.
As i understand, You mean about /boot/grub2/grub.cfg file?