In my opinion there whould be no isses running bothe the 3.0 and the 4.0 version side by side. 3.0 is for framework version 2.0 and 4.0 is for freamework version 4.0.
I guess there is something in the installation program that has not been updated in the new release.
Side by side execution would allow for a smoother upgrade as you simply install the new version, then update BizTalk with a new adapter (Schedule4) and then start to configure receive locations that uses the old version of the adapter to use the new one.
After that you can uninstall the old version if you want to.