Oki, thanks. Now we are getting somewhere.
1) if the boot picture does not disappear, it indicates the boot process has not reached its end where the ShowAmiga96_Close program is executed from WBStartup. This program is supposed to close the boot picture.
Therefore close the picture manually by pressing the 'ESC' button to see what is happening in the background. Usually, the boot is halted by some requester or some kind of error message which you should be able to see as soon as you close the picture. (You might want to disable the boot picture in startup-sequence as well).
Similar problem happened to me with WinUAE 1.4.0 too. When I closed the boot picture manually it turned out the desktop was loaded in native AGA mode that triggers lots of error requesters, even a crash sometimes. This is because WinUAE 1.4.0 changed some screenmode identifiers and screenmode.prefs saved by previous versions of WinUAE might not be compatible with the current version (as was already described here
The only possibility is to try to boot with WinUAE 1.4.0 and start the SYS:Prefs/Screenmode program, select the screenmode as you was using before and SAVE the settings. Then reboot. Next start of AmiKit should boot into correct screenmode again, even under WInUAE 1.4.0.