Hello and welcome!
Yes, there are several programs running in background which might prevent Intuition to re-open screen. LimpidClock, the clock+calendar in upper right corner, is on of them.
Anyway, the most easy solution is to SAVE your new screenmode settings (after you tested it, of course) and then just reboot.
Also, I recommend to turn of startup picture - as it is fixed to certain screenmode. If your desktop screenmode is different, then there are screenmode switches on AmiKit boot which might delay the whole startup. To turn off the bootpic, run MorpheuZ and select Startup Control > Startup Picture.