An experimental version is available.

More information:

http://rammichael.com/7-taskbar-tweaker-experimental-version-with-partial-windows-8-1-preview-support

The startup key resides in the following branch:
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run

Name: “7 Taskbar Tweaker”.

From what you're describing, it seems like the registry entry that makes the tweaker run at startup resets upon restart on your system.

I don't know why that happens, but you might want to place a shortcut of the tweaker in your startup folder instead and see if that works for you.

That doesn't make sense, the "Run at startup" checkbox merely removes/sets a registry value. It shouldn't affect options like volume control.

Possible with Taskbar Inspector.

First, there's nothing to "fix". It's not broken.

The tweaker assumes many things about the target OS. It cannot be easily ported to the new Windows 8.1, it's a time consuming task.
The same thing was done for Windows 8, and now it seems to work equally on both 7 and 8, but in fact there are many places where it does different things under the hood based on the Windows version.
The port to 8.1, though, will probably be easier then the port from 7 to 8 was.

Second... what's the rush? The preview version was released just yesterday.

Windows 8.1 is currently not supported.

Every time you navigate to a folder in explorer, it changes the window’s Application ID.
It has different Application IDs for some folders, e.g. Control Panel. Navigate from any folder to Control Panel, and you’ll see it makes an independent group. Then navigate back, and you’ll see it return.

I remember trying to prevent it from changing the Application ID if the navigated folder is not a special folder, but couldn't find a good solution.