Had the same issues:
Apps > Startup menu is missing in Windows 11.
Unable to change startups via the "task manager"->"Startup Apps",
Disabled startup control in "Phone Link".
Finally found the solution by comparing "Policy" settings in the registry with a working computer.
Found that Registry location [HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\System]
was empty and my working laptop had 22 entries.
I did not go one by one through the entries, so I do not know exactly which one(s) fixed the issue.
Guessing it was one or more of the entries that have "Startup" in them.
"EnableFullTrustStartupTasks"=dword:00000002
"EnableUwpStartupTasks"=dword:00000002
"SupportFullTrustStartupTasks"=dword:00000001
"SupportUwpStartupTasks"=dword:00000001
Here are all the entries in my registry location:
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\System]
"ConsentPromptBehaviorAdmin"=dword:00000005
"DSCAutomationHostEnabled"=dword:00000002
"EnableCursorSuppression"=dword:00000001
"EnableFullTrustStartupTasks"=dword:00000002
"EnableInstallerDetection"=dword:00000001
"EnableLUA"=dword:00000001
"EnableSecureUIAPaths"=dword:00000001
"EnableUIADesktopToggle"=dword:00000000
"EnableUwpStartupTasks"=dword:00000002
"EnableVirtualization"=dword:00000001
"PromptOnSecureDesktop"=dword:00000001
"SupportFullTrustStartupTasks"=dword:00000001
"SupportUwpStartupTasks"=dword:00000001
"ValidateAdminCodeSignatures"=dword:00000000
"ConsentPromptBehaviorUser"=dword:00000001
"undockwithoutlogon"=dword:00000001
"dontdisplaylastusername"=dword:00000000
"legalnoticecaption"=""
"legalnoticetext"=""
"scforceoption"=dword:00000000
"shutdownwithoutlogon"=dword:00000001
"SlowLinkDetectEnabled"=dword:00000001
Good luck.