I create a patch (.MSP) with two Windows Installer databases using MsiMsp.Exe and PatchWiz.dll, shipped with Platform SDK and .PCP file.
When I try to apply a patch, Properties of Windows Installer Repository is patched, but all components, including files and registry keys remains from old version.
Code for every component in Target and Upgraded components differ.
In every system installed Windows Installer 2.00
If it helps, I can create verbose logs for any operation.
Patch Creation Properties file (.PCP) I use when create a patch.