Hello Robert,
Thank you for the screencast, which shows the problem(s) very clearly. I logged a defect about both problems you described:
1. SectionTool handle appears way too far outside to be helpful.
2. After a view switch, Section Tool does always keep the initially selected mode and doesn't allow to select another mode anymore.
The problem was not easily reproducible with my test projects. Would it be possible to contact you directly to get access to your project in order to investigate the problem on your project? We could try to solve it otherwise, but being able to reproduce it exactly as in your video would probably be the fastest way to find the reason.
Some first workarounds that might help until we have a proper fix:
For 1.:
Using the ViewCube menu (arrow-symbol at the bottom-right corner of the view cube), you can switch to perspective camera. This makes it possible to move inside a building without section plane.

For 2.: If the SectionTool refuses to reset, a page reload will reset the viewer state and should help here. In Design Collaboration, a page reload preserves where you are (e.g. package, team, selected viewable etc.)
Henrik Buchholz
SW Architect
Autodesk