I am noticing this behavior on Server 2019 starting in May 2023. The window appears multiple times throughout the day, but disappears so quickly that I can't see what program ran. My first instinct was to check for malware. My MalwareBytes scan came back clean.

I enabled the audit process tracking in my security policy, and when I saw the window flash I quickly went to Event Viewer and there I saw SecureBootEncodeUEFI.exe.

I am seeing SecureBootEncodeUEFI in the Task Scheduler configured the same way as reported earlier in this thread.

Can someone from Microsoft explain what this executable is doing and why it has started running multiple times a day?

You might be in Setup Mode because you have deleted the Platform Key in your BIOS. Enabling Secure Boot in this state enables your OS to write a new Platform Key (possibly useful for securing a Linux installation). But if you don't do that, you remain in Setup Mode and the Secure Boot State, indicating the Platform Key has been used to secure the system, will remain off.

Your BIOS might have an option to restore the default Platform Key, possibly called "Restore Default Secure Boot Keys", which restores the Microsoft Key. After doing that, your Secure Boot State will be On when booting Windows.

Good code for Windows 10 too of course and should handle most conditions including legacy or missing key and exception, as well the future.. Prints to console whilst also returning the flag for batch or script use:

using System;
using Microsoft.Win32;

namespace CheckSecureBoot
{
    class Program
    {
        static int Main()
        {
            int rc = 0;
            string key = @"HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\SecureBoot\State";
            string subkey = @"UEFISecureBootEnabled";
            try
            {
                object value = Registry.GetValue(key, subkey, rc);
                if (value != null)
                    rc = (int)value;
            }
            catch { }
            Console.WriteLine($@"{subkey} is {(rc >= 1 ? "On" : "Off")} ({rc.ToString()})");
            return rc;
        }
    }
}