Someone could have taken that specific build, added malicious code and spread it. Of course the original binary looks 99% the same as the malicious one. AV software should detect the malicious one and therefore the original one is collateral damage.
If your binary is signed all of the above still can happen. But a malicious modified version of your code will never have a valid certificate.
Every false positive that was detected as such will improve the reputation of your certificate. Everytime that a binary signed by your certificate runs (and does nothing malicious) will improve your reputation. Everyday that passes will improve your reputation. And if your reputation is high, it doesn't matter how closely your binaries look like malware and therefore false positives will decrease rapidly.
Since you already have a certificate (MC22.exe in System32 is signed) it should be relatively easy to sign the other binaries.
But note that even a signed binary is still a possible threat, mainly because of exploits. Therefore any technology that prevents exploits is a reason for AV software to monitor your software less aggressively and therefore minimizing incompatibilities. Such technologies include ASLR and DEP. I would recommend to enable them.