Solved Installed Windows 10 as second OS. Now 8.1 has Problems

I installed Windows 10 on its own ssd as a second OS so I could use DX12. After I got all drivers installed and everything setup in Windows 10. I booted back into my default OS (8.1). For some reason it loaded a bunch of startup programs that I had disabled previously. So I disabled the startup items and restarted the OS. My changes did not save so the Items booted again and were still enabled. So I tried booting in safemode and diagnostics mode and tried making the changes again and that did not work either. When I opened Opera browser to google a solution I noticed that my theme and all of my shortcuts were missing but bookmarks still intact. When I added the shortcuts and theme back to Opera they did not save. Next I attempted a system restore but of course it could not find any previous restore points. Everything else as far as programs, games and drivers seem to work fine. I don't know what to do next. I have had this OS installed for about 2 years with no problems and is my main workstation with years of apps, configuration, files, tweaks, etc. setup exactly how I like and I dread doing a clean install. I would be grateful for any advice.

Disable the Windows update service. It's probably reloading your stuff every time you try to change it. Go into Services, find Windows update, right click it, choose stop, look in the tabs for telling it to not restart and set it to disabled for now. When you need it for updates just go back in there and start the service manually.

Thanks for your reply Carri. I finally figured it out. I had 2 different malware viruses. I found one with Super Antispyware and the other with Malwarebytes. I don't think It had anything to do with my installation of Win10 but I had never acquired a virus in the 2 years I've been using 8.1 so I never thought that was the the issue. I don't know how or why but after installing Windows 10 my Win8.1 was infected maybe just coincidence. Oh well, at least everything is normal now.

There is a whole new breed of malware out now, they are called Apocalyptic Viruses and Trojans. They can get past your best security and protection programs. They use both rootkits and other methods and can lock down and destroy your drive. I had it happen on one recently and had to reformat the entire drive and reinstall the OS. Be very careful where and what you download. They attach a small trojan to an install file and that's usually what starts it, it will download all kinds of malware and install it while you're installing your program. The file will read clean by almost every antivirus out there. So you think it's safe to install. They are using a masking worm. Really becareful. It's a newer breed.