I think what you had was a two-fold problem.
First was putting your QB64 into a system folder (C:\Program Files and C:\Program Files (x86) are both considered to be system folders and thus have enhanced security and reduced permissions on them. It's best not to put anything there yourself, as those tend to be "Read Only" access type areas, with all the data files that pertain to them in your AppData folder or MyDocuments folders. EXEs, like QB64.EXE, tend to run into all sorts of issues when trying to write to either of the Program Files directories themselves. That's not to say that you can't do it -- but you can only do it by tweaking permissions, and then being prepared to retweak those exact same permissions every time Windows does an update and resets its security settings.)
By moving your QB64 folder off to a non-system area, such as to C:\QB64\ you should be able to get rid of any issues with the permission levels and UAC causing you problems. (Exception might be with a removeable drive, as Windows might have ownership of it tagged as belonging to another person/PC, which you'd need to overwrite first.)
Your second issue appears to have been with your antivirus speaking up and saying, "I don't know this EXE! It must be bad!" Of course it's not going to know an EXE which you just compiled and created -- its an EXE that's never existed before to get listed in their database of "Okay Products". The antivirus speaks up, quarantines or deletes the file, and causes issues. In this case, it sounds as if your anti-virus has some pretty strong permissions and an incredibly heavy hand, as it seems as if it keeps setting folder permissions and all to "Read Only", even after you've manually went in and changed them! The only way to get around this type of issue, is by whitelisting your folder and telling your antivirus to, "Buzz off! These are EXEs I created! I didn't write myself a virus, you dumb software!!"
As long as it's your PC, and you don't plan on letting everyone in the world use it (such as a library computer, or one in the cyber-cafe coffee shops), you should be more than fine by setting permissions to "Everyone", as you mentioned above. Basically, "Everyone" is an user base that says, "If they can log into this computer, then they can access these files." Since QB64 isn't your top secret porn folder which you need to hide from your wife and kids (at least, I hope it's not), there shouldn't be any real issues by assigning full read/write permissions to "Everyone". After all it's just "Everyone who can log into this PC," and chances are, if someone can already log into your PC, then they can just alter permissions or ownership already, so all those other security features that make you jump through hoops are honestly nothing more than a PITA to begin with.
