And it isn't, for instance, files that the programs have saved after the first analyze that are recorded as added?
No it's not, this is exactly what I did in this order (I didn't open any other programs, etc., because I know they'd taint the analysis of an installation):
1. Did a before install analysis with ZSoft Uninstaller.
2. Installed .NET Framework 3.0 (and subsequently waited forever for it to install).
3. Rebooted.
4. Opened Internet Explorer and went to Microsoft Update and downloaded and installed two updates for .NET Framework 3.0.
5. Rebooted.
6. Did the after install analysis with ZSoft Uninstaller.
7. Looked at the ZSoft Uninstaller log, and noticed right at the beginning of the log were files which were already in existence on my hard disk were logged as newly installed files.
It is indeed very strange!