What you see and have access to in the bios, is not everything that's IN the bios. The many hidden settings. Bios is the basic machine operating system, it says what is what and where things are. Cmos is different, but often confused with bios. Cmos is the extra commands from windows that change or contain a list of the bios settings.
From a cold boot/reset, the pc will use bios, it'll search out all your equipment and apply any settings it has. When you shutdown by windows, that list gets saved to cmos and on a regular startup the pc applies cmos as the startup. Much faster, as the pc doesn't have to hunt down, verify, check your stuff.
You used software to change bios settings. Even removal of that software will still have the settings saved in cmos, so that's what you need to clear, which forces bios to do a reset and cold boot from scratch, as now there's no startup cmos list to apply.
I'd also run ccleaner (piriform.com) and run the registry tool (say yes to backup) to clear any temp files, orphans, associations that software might be trying to enable as windows doesn't actually delete anything, as such.