No, the installation is fine. This problem is typical.
Program A's files is in C:\Program Files
Registry is in C:\Windows\System32 (let's say)
When you upgrade, C:\Windows is overwritten, some useless WIN98
files are left behind. However Windows installation does not touch
C:\Program Files.
So, without the registry, (which stores the list of programs
installed), Windows does not even know that Program A exists!