If I put a link to the PL/SQL Developer exe in Windows' Autostart folder, it is not displayed in the Task Bar right after start.

The application is up and running, but needs to be put to foreground with Alt+Tab once until it's also visible in the Task Bar.
We'll investigate this. Can you let me know which PL/SQL Developer version you are using?
I'm using the latest 14.0.0.1961 on a fully patched Win10 Pro.
It seems to work fine. I tried the following:

1. Run shell:startup to open the startup folder
2. Copy the PL/SQL Developer shortcut to this folder
3. Add a userid=username/password@database parameter to the shortcut
4. Restart the PC

This is on a Windows 10 PC. I tested this with both the 32 bit and 64 bit versions.

Can you confirm that this matches your scenario?
In the initial scenario I did a manual connect to DB, but I also tried it with the username/password parameter right now.

In both cases - with and without that parameter - I see the issue described in my first post.

I'm not sure, whether some other programs also auto starting interfere with PL/SQL Developer in the given scenario. On my machine there are a few that also auto start, Outlook and Firefox among others.
Behavior got a bit worse after the recent Windows 10 2004 Update with PL/SQL Developer 14.0.1.1965:

Even if I start the Developer manually from the Startmenu (no matter if attached or from app-list) the task bar entry generally disappears after "splash screen" is gone. It looks like the initial task bar entry IS the "splash screen" entry, which is supposed to disappear after successfully starting the program.

Still the task bar entry of the main application is not visible until it is brought to foreground with Ctrl+Tab. Behavior at auto start is still the same.

This is fixed in Version 14.0.2.1969 (64 bit).
This seems to be a revenant. I see this behavior again in version 14.0.4.1982. It usually occurs at first start of PLSQL Developer after booting the system (w/o any autostart stuff involved).

The reproduction scenario differs a bit from my initial description. Currently I start the Developer manually, but using it mostly on my second desktop (Windows 10 Pro 2004, Build 19041.572). I don't know, whether this relates to the faulty behavior.
Still there in Version 14.0.5.1986.

It's not about "Autostart" and "after system boot" anymore. As tested again right now, it happens at every Developer start. It doesn't matter if it's started on the first, second or whatever virtual desktop on Win10.
This occurs also in Version 14.0.6.1988 (64 bit) - Windows 10 Pro 20H2, Build 19042.1237

Even when opening a second Developer instance, it doesn't appear right away in the task bar. To mitigate this, all other windows have to be minimized and a click into the window of the "missing" Developer instance, makes it available in the task bar.

After all these investigations, the correct Thread title should rather be "PL/SQL Developer not shown in Task-Bar after program start". Unfortunately I can't change that (or didn't found the right button).
Is there any possibility to support reproduction of the problem?
This still occured in the new Version 15.0.0.2050 (64 bit). But after going through the preferences I found an option, that triggers the behavior. If you set User Interface > Options > Autosave desktop to "off", PL/SQL Developer is displayed in the taskbar as expected after start. If you set it to "on", the behavior is faulty again.
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