Installed 4.01b on primary machine, where I experience no-autostart issue (I don't have that issue on secondary machine).
No registration pop-ups, but can confirm auto-start is not fixed. Reset to 'automatic (delayed start)', which solves the issue for me - rather than doing the reg tweak thing - and all is OK again.
I wonder if it isn't due to Emsisoft new Firewall Fortify feature that is causing some sort of delay? I do have VS processes excluded in EAM, and don't get any warnings, but maybe there is some sort of delay there interfering with the automatic start. IIRC there are other reports of (I think different) issues by other users of EAM on Wilders. Just a shot in the dark.