Maybe a little bit late, but today I'd made the change (for the fourth time) from XPSP3 to Win7. The new Simatic Manager 5.5 was installed without a problem. WinCC flex 2008 I made some changes in the configuration.
First of all you have to right click on the setup.exe in the root folder and go to "properties". At the "compatibility" tab you set the modus to Windows XP SP3 and close by clicking OK.
The first problem during installation was the Windows installer 3.1 error, because Win7 uses 5.0. This I solved by going to /CD_1/MSI and opened the MSIInstallerW.ssf in Notepad.
By default, the "isCriticalComponent" value is set to 1. Change this one to 0, save and start the setup.exe in the root folder. Now you will see that the Windows Installer is skipped and all the rest will be installed normally.
You can choose to install all applications separately, but I needed to run the complete WinCC Flex 2008 installation to let run WINCCSQL stuff properly.
Upgrading afterwards to SP2......no problemo.
I hope this will work for those people who still have sleepless night to get WinCC Flex 2008 running in Windows 7.