Important to know is that the Thinstall version build 3.396 does not work with the new features ‘Application Link’ and ‘Application Sync’ of ThinApp RC build 3.396. These features are only available in ThinApp.
Beside it there are a few obvious enhancements like a default isolation mode which is set to Merged and an option VirtualComputerName. These enhancements give you the opportunity to virtualize more and more applications than before.
A full list of added enhancements for RC (Build 3.396) can be viewed here.