I cannot reproduce the problem in any way. I just tried uninstall/reinstalling using the same installer that is online now, and there are no problems whatsoever.
I also tried to switch from night/day, and no problems either. Of course, we would have noticed such issues, since we are been using on it for the past months, starting FSX like hundreds times at day...
Try to uninstall and reply YES to the question "Do you want to remove the Addon Manager ?" and "Do you want to remove the Couatl engine?" that are made at the end. This will do a more clean reinstall.
Of course, the usual suggestions about disabling the antivirus during the installation, and configuring it to exclude the sim folder from scanning, are always valid.