Issue has been feedback to try and determine the simpliest work around if indeed the cause is the limited number of slots. Some of use are dubious since we have systems that shouldn't be using more than a few apps that would register for that ability.
Please continue to use the Send Feedback mechanism to raise the issue. That is filtered to the Developers as part of that process, and is much more efficient than having them try to read all the forum posts.
When anything definitive is determined, we will update this thread.
[Marked as best answer simply to allow this post to be the most visible until a true answer is obtained.]
Update #1: Although there are several ways to force the "enabling" of the green ticks, I am not going to mark them as part of any Best Answer- yet. There are definite downsides to employing them for the average user. I would prefer to wait a bit to see if there are any other better methods before impacting people. Of course the readers of this thread are free to read about those methods and employ them. The lack of the ticks are annoying, but far less than some of the potential impacts of the fixes.
Update #2: This issue only seems to be triggered by doing an update over top the existing previous installed version. As @LarryLACa rightfully pointed out, for almost everyone doing the full uninstall first, then followed by an install does ensure that the various missing "features" are created. Once installed be sure to verify that the B&S configuration parameters are the same as before you uninstalled. B&S will detect that you already have data in your Cloud, and it will see that the folders/areas on your computer you have B&S watching might be the same. It will ask you if you wish to merge what your computer has at that point, with what it also sees in the Cloud. Then B&S will take time to go through the selected folders on your computer to crosscheck them with what's in your Cloud, but there will be little to no real "uploading/downloading"- just the crosscheck of file/folder name/size/date/time stats. [Unless some data actually changed].
As @LarryLACa indicated, it would be best if everyone being affected used the Send Feedback option inside B&S to highlight your problem before doing the uninstall/install- and check the box for including system information. The more data the Developers have from as many people as possible, the easier it will be to figure out all the required trigger conditions for the problem- and thus how to correct the issue.
Update #3: Although performing an uninstall/reinstall definitely corrected the lack of registry entries trigger for this issue, there were still some users that might experience loss of the tick marks. The April 17 2018 Release Notes for Version 3.41.9267.0638 indicate that all underlying conditions should now be corrected. This version was released this week. I was able to successfully install the new version on top of the 3.40 version- no uninstall is required.