The things people hit most, and what to do about each.
Click More info, then Run anyway. This box appears for any program that has not been signed with a paid code-signing certificate. It is not a virus warning and it does not mean anything was detected. You are right to be cautious about that box in general.
Open the folder, hold Shift, right-click an empty space and choose "Open PowerShell window here". Paste this and press Enter:
powershell -NoProfile -ExecutionPolicy Bypass -STA -File .\ApexTweaks.ps1
The error message will stay on screen this time. Send it to support and it will say exactly what went wrong.
30 of the 110 tweaks change a setting for the whole PC (GPU scheduling, power plans, Windows Update and browser policies, a few services), and so does creating a restore point. Those are marked ADMIN. Everything else works as a normal user. Use Launch APEX TWEAKS (as administrator).bat, or press Restart as administrator on the Settings page.
That is correct and deliberate. Measuring real frame rate needs Intel PresentMon, a free separate tool. Download it from github.com/GameTechDev/PresentMon, rename the program to PresentMon.exe and put it in the same folder as the app. The app will never show you an FPS figure it did not measure.
Open the Restore Centre and press Undo Everything. Every setting goes back exactly as it was. If one change in particular is the problem, the change history on that page lists them in order with timestamps, so you can see what happened when.
The two most likely candidates: visual effects set to performance (Windows looks plainer, which some people dislike), and GPU scheduling (a small number of older drivers do not get on with it).
Two of the changes only finish applying after a restart, and the visual effects change needs you to sign out and back in. If something still looks wrong after a restart, make a ticket in our Discord and attach your change log: the Settings page has an "Open my data folder" button and the log is changes.log.
discord.gg/WVKUu2PSc
changes.log to your Discord ticket. That file says what was changed and when, which answers most questions immediately. The Settings page has an "Open my data folder" button that takes you to it.