WinUAE 1.4.0 changed the identifiers of all screen modes (except 640x480, 800x600, 1024x768, 1280x1024). This results into incompatibilities between screen mode preferences saved with pre-1.4.0 and 1.4.0+ versions.
If you install WinUAE 1.4.0 or later versions, several pre-configured screen mode presets used by "ScreenMode AmiKit" tool might no longer work and AmiKit might not boot into correct screen mode anymore.
It might also happen that as soon as you install WinUAE 1.4.0, the boot picture never disappears. If you press the ESC button to close it manually, all you can see is a grey Workbench screen.
If this is the case:
1) please use WinUAE 1.3.2 again, boot AmiKit, run "Screenmode AmiKit" and select 1024x768 mode. This mode should be compatible even with later WinUAE versions like 1.4.0.
2) Then install latest WinUAE version again and your AmiKit should boot into 1024x768 screen mode without any problems.
3) Now, you can change to your preferred screen mode again. Run "Screenmode AmiKit" tool, select your mode BUT before you reboot start the system's AmiKit:Prefs/Screenmode program as well and select and SAVE the same screenmode there.