I've downloaded and installed the latest release of SQL Compare.
SQL Compare 10.0.0.140 Professional Edition running on Windows 7 Enterprise 64-bit.
All seems well apart from the Source / Target selection window when editing a project or when opening an existing project created under SQL Compare 10.
I originally selected the Source Control -> Scripts folder option on both sides of the comparison, performed a comparison and then generated a synchronisation script. I then decided to select 'Edit Project' at which point the Source / Target selection window was displayed and none of the source or target options radio buttons were selected. I selected the Source Control -> Scripts folder options again and the 'scripts folder' entry box was blank on both sides of the comparison, forcing me to re-select the two folders, extremely annoying if you need to iteratively make refinements to the project settings.
I see the same behaviour when opening an existing project created under SQL Compare 10 - none of the originally-selected source/target options are selected.
SQL Compare 9 does not show the same behaviour when used with the same project file - i.e. the previously selected source and target options are pre-selected when opening an existing project file.
I'm happy to email a copy of the project file or screenprints to help troubleshoot the issue if required.