The problem is that IPrefs sometimes crashes during the startup and the message about the crash is displayed behind the boot picture. So it looks like the AmiKit is still booting. Try to press Esc to quit the boot screen and you would be able to see what is happening behind the picture.
Or reset AmiKit and try to boot again.
You may also try to disable cat-boot screen completely, edit s:startup-sequence and disable this line:
by putting ; in front of it, so it will look like this
Anyway, 1280x800 works here without any problems. If 1024x768 works for you, then use classic SYS:Prefs/Screenmode to switch to your desired screenmode. It should work, just watch out for IPrefs crash.
The cat-boot picture is not adjusted for 1280x800. This means it opens the picture in other screenmode. Then several screenmode switches must be done when booting (to switch to DOpus registration screen, then back to boot-screen and then back to desktop again..). This slows down the boot process. To avoid this, disable boot-picture as described above or adjust the boot-picture to your 1280x800 screenmode in AmiKit:Prefs/ShowAmiga96_Prefs
EDIT: COMPLETE MANUAL HOW TO SWITCH TO NOTEBOOK WIDE SCREENMODE IS HERE: