But when I was uploading the exe to VirusTotal.com, there was usually one false positive - often Microsoft with "Win32/Wacapew.C!ml" named. As we know, the "ml" at the end means "machine learning", so it's not actual real malware but just a bad guess that it is. Take a look:

Now, quite frankly I was getting tired of submitting my exes to Microsoft for white-listing, and so I signed up with VirusTotal.com to upvote my own exe (because you can't upvote without a VirusTotal account). However, I then realised it showed me WHY my exe was flagged: it was matching a UPX rule! There was an icon to click at the right of this ruleset (not shown in the screenshot above), which literally SHOWED ME which byte sequence was causing the false positive! I tried changing the first byte in the sequence but my exe wouldn't run, so I changed the second instead (from 00 to 01) and now my exe ran again. Take a look at what I changed (you might need you right-click and open the image in a new tab):

I then re-uploaded this new modified exe to VirusTotal and NO FALSE POSITIVE! Just from changing one single byte in a 3 MB exe! Look:

I hope my experience can help someone else fix their false positive issues.

I'm actually going to code a small app to auto-change that 00 to 01 in my build process, so my exes will NEVER match that ruleset again.
