This is a follow up message. I got to thinking and I have a possible avenue for you to explore to track down this problem. It relates to your installer.
Normally, unless I really trust the S/W developer, I go through a deep uninstall using Uninstaller Pro, followed by a reboot, before installing an update. I find this avoids many problems. But this time I didn't. I just installed directly over the existing software. It occurs to me that your installer might not be either fully testing error conditions or leaving some old artifacts in place, like installed system services or dynamic link libraries. As info flashed onscreen it appeared that your installer was at least trying to do some cleanup, but as a S/W developer myself I know this is hardly error proof.
Anyway, this is at least something to consider. The quality of your software convinces me that you really do know what you are doing, so the issue might be fairly subtle.