I modified the Start menu item for Notepad to start minimized and it works - i.e. starts minimized when started from the start menu.
P.S. When adding a program, the execution tab is not available until you add it and then edit its properties.
Invoking run from within a running SO (which was started as admin) starts the program according to the setting - normal or minimized. I'll need to run further test on a VM, can't be rebooting my primary machine everyday - it controls too many things :-)
I noticed that SO now request admin privileges when started. That's understandable because it needs that to monitor the keys that only admins can see. This presents a problem though. After starting SO, if you run a program from within it, that program inherits the admin privileges. More often than not, you do NOT want this. Not sure how you'd solve this issue.
An enhancement would be to add a check box for [x] Run with highest privileges. Win 7 Task Scheduler allows this and I use it to start the few old programs I have that must be started as admin. Checking that box will start the program and avoid the "do you want to allow" prompt. Not sure if that ability is restricted to Task Scheduler or not.
Thankfully, ctrl somehow runs without admin privileges so controlled startup programs start the way you would want them to.
I tested Controlled Startup - I added Notepad, Wordpad and Paint. The first was set to minimize, second - normal, third - maximize. All of them started exactly as setup. The only probable difference - I didn't reboot, I simply used Tools - Run all Controlled Startup items.
Can you try this was as well - there should be no difference between reboot and this menu.
Regarding administrative priveledges - yes, this is so. Frankly, I searched on methods to run programs in normal mode, but didn't find it yet. I will continue searching.
Regarding running as admin. How does ctrl get started when I boot? It seems to be launching controlled items as a normal user. That's my assumption. I have one program that doesn't work properly when run as admin so it's the tool I use for testing. It's what convinced me that ctrl was running programs as a normal user while running from within SO ran them as admin.
But, I will note that without being registered, minimize on start-up does not work. Earlier this evening I was repeatedly starting SO but it would not minimize. Just now after entering my key, I exited and restarted for good measure and behold it minimized. FYI.
Admin rights - Ctrl.exe starts normally - it doesn't have so-called "manifest" that tells Windows to start it with administrative privelegdes. Therefore, all applications it starts inherit the same mode.
SO.exe starts in administration mode because it needs access to all Registry entries for their modification. And all apps that it starts inherit the admin mode by default. This is the difference.