The Migration tool is a 3rd party program that fools installer that do not know about P3D, to think they are installing into FSX, that seemed to be the most likely explanation, considering you said the installer doesn't install into the P3D directory.
If you never used it (are you *sure* ? not even in the past ?), that might indicate your P3D installation or its registry key is not correct, but of course is difficult to say, since your description was so vague.
Please clarify all the following:
- What's your P3D version ?
- Do you use the current version of our installers ? Only the latest versions supports the latest P3D releases.
- Do you see a request to install into P3D, or the installation goes directly into FSX without asking ?