I decided to install the new version and run a scan. Unfortunately, when the scan finishes the 'system scan' window freezes. It doesn't have 'not responding' status but it's just there and I can't click anything. The rest of Spybot still works though.
EDIT: I found the problem. It was offering to disable third-party cookies but the window was practically hidden underneath the 'system scan' window and I could barely see it. It would be more practical to make it by default on top when these type of notifications appear.
I also have to add that I'm with the sentiment that all the separate windows instead of being integrated into a single one is abit odd.