I just started playing Morrowind again, and I installed it via GoG. I also installed OpenMW and a bunch of visual mods.
My problem now is that every time I start Morrowind, either through GoG, or OpenMW, the game disables my Win7 visual themes, and I can't get the themes back when I close the game.
I've looked around, but I haven't found a solution besides rebooting the computer.
The .exe file that GoG uses has the options of "Disable visual themes", "Disable desktop composition", and "Disable display scaling..." greyed out, so I can't change that.

Does anyone know a fix to this? I don't want to reboot everytime I'm done playing Morrowind.

Never heard of this happening. Disable all mods. If this helps, re-enable them one-by-one, to find out which one is causing the issue. If it doesn't help, uninstall Morrowind and all mods (ideally making sure that everything has gone completely, including registry entries), and then re-install Morrowind without mods, and try again.By the way: Are you using Galaxy? Then you might try installing and launching Morrowind without Galaxy.
Where and how exactly does your exe let you do all these things? Which exe? My morrowind.exe doesn't.

I installed Morrowind through GoG Galaxy, but I've had the problem happen both when using Galaxy and just starting the game through the .exe.
I also don't think the problem is due to mods, because the standard Aero Windows theme gets changed to a simpler one as soon as I start the "Morrowind Launcher.exe". I've added a screenshot of my "Morrowind.exe", which shows the options for disableing things greyed out. That is the same with the "Morrowind Launcher.exe".

I have Morrowind on CD, so I could try installing it that way, I just used my GoG version so that I don't need to use the CDs.

Edit: I think I might have found a way to solve the issue. When I start the game through Galaxy, it tries to start the game, but nothing happens. I used to just end the "Morrowind Launcher.exe" task, and start the game again, which made it work. The problem then was that I was stuck with the Basic Windows theme, and not Aero.
What fixed it was if I used "End Process Tree", instead of just "End Process". I can start the game just fine using OpenMW, which I was using anyway.
I don't know why the problem only happens when I don't use OpenMW, but atleast this way I don't have to reboot everytime I've played Morrowind.

Thanks. I noticed that your Compatibility Settings options are different from mine (Win 7 vs Win 10? - but I don't think that Win 7 causes the problem).
Your screenshot reminded me of something I've seen before, but not in the context of Morrowind or another TES game. It must have been quite an old game (from the Windowes 3.1 or Win95 days) which has problems with Win 10. It didn't work, and then I changed the compatibility settings (changed compatibility to an older Windows version, changed DPI settings, etc.), which also didn't work, but at one stage the compatibility settings box looked like your screenshot, and I couldn't do anything with it. In the end I un-installed the whole game completely. Not encouraging for you, I know, but perhaps someone else has an idea what might cause compatibility settings to be ticked, but greyed out. At least I'm very convinced that the problem is unrelated with Morrowind itself (which I've been playing from its release until today on several PC's running very different OS's, CPU's and graphics (including integrated cards) without ever encountering a really serious problem.
That it doesn't happen when you run OpenMW is probably because OpenMW either doesn't use the Morrowind.exe and its compatibility settings (except to check it for existence), or just uses it in a way which doesn't "alert" the compatibility settings.

Create a copy of Morrowind.exe as Morrowind2.exe, for example.
You can change compatibility options for a copy.
Run the game from Morrowind2.exe

You can also try to change Morrowind folder name (to 'MorrowindGOTY', for example) or copy game to another location.
Then, compatibility options will not apply to the game and you can set them manually.

Of cause you don't have problems with OpenMW, because compatibility options (that GOG installer or Galaxy set) don't apply to OpenMW.exe

I tried using a copy of the .exe, and it worked both with Morrowind.exe, and Morrowind Launcher.exe.
I'm using OpenMW to manage the mods I have, so I'll just keep using that, but thanks a lot to you guys for helping me.

If you'd like to remove the compatibility settings being forced onto you, you could remove entries for things from the registry in the following locations. (Sometimes renaming a game's executable to avoid the compatibility settings can cause problems)

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers

HKEY_CURRENT_USER\Software\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers

HKEY_CURRENT_USER\Software\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Compatibility Assistant\Persisted

In those locations you'll find paths to program executables. So look for any pointing to your Morrowind.exe (for example.. "D:\Games\Morrowind\Morrowind.exe") and delete it.

I'm not sure if I've remembered all the locations where such things are stored, so if removing it from those locations doesn't solve it you could search the registry for the path of the game's .exe, such as the example I used above, then see if any of the results look like compatibility settings such as those you would find in the above locations.

I also seem to recall GOG goes rather crazy/lazy with these things, even adding entries for files and not just programs. Using it when not needed, or even when it actually causes problems.

Note, not all compatibility settings that are stored in those locations are applied via the File>Properties dialogue box, for example DEP/BEX exceptions are applied from Computer Properties>Advanced>Advanced>Settings>Data Execution Prevention.

I feel that's rather hyperbolic.

Deleting registry entries is no more risky than deleting files, delete the wrong file and a program, or even Windows itself, could fail to work.

It is not likely to create problems, any more than deleting a file, it depends entirely on what is deleted.

There would be no point in editing the entries mentioned after uninstalling the software, and the entries likely then wouldn't exist anymore unless whoever made the installer was lazy.

If the person wants to reapply the compatibility settings after deleting them they could add them manually like normal, or reinstall the game, or restore an export.

Anyone unfamiliar with the registry and the potential risks probably doesn't know how to access it, information I deliberately left out for that reason.

As for Morrowind's registry entires, you could delete them all and the only loss would be some game settings which would be forgotten and reset to defaults (such as resolution, volume levels, AI distance..).

So you say - and I wish you're right. I agree that editing the registry is not an issue for people who know what they are doing. Unfortunately, not all people understand the registry, and not all of them keep their hands off the registry. Those people are the target group for my word of caution.
Let's leave it at that. I'd be more than happy, if my target group were empty and my remarks were unnecessary.