At this point I can't think of much more that hasn't been suggested already. If you are positive that your installation is not corrupt, the most likely issue may be a dependency problem. You could
- re-install the VC runtimes. I don't have the Orbiter 2016 installation package to hand, but I think that the correct VC runtime redistributable installer was included (at least in the zip installation package).
- create a minimal scenario, including a single simple vessel (e.g. ShuttlePB) that doesn't add any unnecessary dynamic dependencies
- create a minimal solar system (e.g. including only Sun, Earth, Moon), also to reduce the number of dynamic dependencies
- if you are keen, you could download a dependency analysis tool such as Dependencies (https://github.com/lucasg/Dependencies) to check for potential problems with direct dependencies (this doesn't check for dynamic dependencies, but we tried to minimise those in the previous steps)
- You could try the latest Orbiter beta (https://github.com/orbitersim/orbiter/releases). This was built with a different compiler, so uses different VC runtimes, which may bypass whatever problems you are having. Also you could try both the x32 and x64 versions to see if it makes a difference.