Smart-Screen filter still complains, despite I signed the executable, why?

Applications that are signed with a standard code signing certificates need to have a positive reputation in order to pass the Smart Screen filter. Microsoft establishes the reputation of an executable based upon the number of installations world wide of the same application. Since you haven't published your application as yet (and therefore the reputation hasn't been established as yet), the Smart Screen will continue to flag the application.

There are two solutions: either wait till the application has a large user base and its reputation will be adjusted by the Smart Screen. However, the current working status might prevent users from installing and trusting the application. The second option is to sign it with an EV (Extended Validation) code signing certificate. Applications signed with an EV certificate establishes its reputation right away. To quote Microsoft:

Programs signed by an EV code signing certificate can immediately establish reputation with SmartScreen reputation services even if no prior reputation exists for that file or publisher.

You can find further details at Microsoft SmartScreen & Extended Validation (EV) Code Signing Certificates blogpost.

If you have a standard code signing certificate, some time will be needed for your application to build trust. Microsoft affirms that an Extended Validation (EV) Code Signing Certificate allows to skip this period of trust building. According to Microsoft, extended validation certificates allow the developer to immediately establish reputation with SmartScreen. Otherwise, for some time, until your application builds trust, the users will see a warning like "Windows Defender Smartscreen prevented an unrecognized app from starting. Running this app might put your PC at risk.", with the two buttons: "Run anyway" and "Don't run".

Another Microsoft resource states the following (quote): "Although not required, programs signed by an EV code signing certificate can immediately establish reputation with SmartScreen reputation services even if no prior reputation exists for that file or publisher. EV code signing certificates also have a unique identifier which makes it easier to maintain reputation across certificate renewals."

My experience is the following. We have used regular (non-EV) code signing certificates for signing .MSI, .EXE and .DLL files since 2005, with timestamping, and never had problems with SmartScreen, until 2018, when there were just one case when it took 3 days for a beta version of our application to build trust since we have released it to beta testers, and it was in the middle of certificate validity period. I have no idea what the SmartScreen might not have liked in that particular version of our application, but there were no complaints since then. Therefore, if your certificate is a non-EV, it is a signed application (such as an .MSI file) that will build trust over time, not a certificate. As in our case, a certificate can be issued a few months ago and used to sign many files, but for each signed file you are publishing, it may take several days for SmartScreen to stop complaining about the file after it is published.