I'm sorry, but I cannot reproduce it and nobody else has reported it (it happened sometimes, but it's not a problem of the installer). Another possible reasons is that your FSX:SE registry keys are wrong or even entirely missing.
This can happen if you had FSX installed, uninstalled it after FSX:SE without reinstalling FSX:SE (which needs to adapt its registry to the new "stand-alone" situation) or if you or another addon not fully compatible with FSX:SE, set the FSX:SE registry keys in the wrong way, only to fool a non-compliant installer to install anyway.
See this reply here, which explains how the registry keys are supposed to be when the sim is installed properly:
http://www.fsdreamteam.com/forum/index.php/topic,14166.msg104727.html#msg104727