Unfortunately, as far as I know, that's the only registry (file) checked by installer. In order to exclude any issues related to this one could you:
- Also check the 64 bit folder (inside Program Files instead of Program Files (x86)) - although it should not exist there
- Try renaming the 32 bit file and launch the installer (or just confirm that this did not help in case you already tried it) - just to make sure there's no other faulty data.
I will try to reproduce it on my side.
1. What version of the executable are you trying to install (latest one on NXP site is 3.0.2.6):
2. Is there any old FreeMASTER entries in "Program and Features" window ? If yes - what version ?

In case it's not displayed, there may still be a Windows registry entry
HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\Microsoft\Windows\CurrentVersion\Uninstall\FreeMASTER 3.0