There’s always a chance failure in regard to DirectVR, hence the hint screen that is shown about that during the scan.
Provided your Skyrim SE is updated to the latest version, DirectVR FOV is applied without scanning, which is the most important thing. Not ideal, but not a major issue if the rotation scan fails. if head tracking feels off, adjust the head tracking sensitivity in the vorpX menu.
BTW: I would recommend to use the original Skyrim. On the majority of systems it runs quite a bit better with vorpX.
Not sure about your Arma III issue, sorry. Works as it always it did. Please mind that Arma III is Z-Buffer 3D only, which provides a less natural and strong 3D effect, but is a lot faster.
If the normal mouse based head tracking is inverted, please check whether you maybe have your mouse axis inverted in the game’s options. If that is the case either change that or use the “HT Invert Y-Axis” option on the head tracking page of the vorpX ingame menu.
Also make sure that you didn’t indvertantly disable the vorpX head tracking in the config app. Doing so might lead to the impression that head tracking is inverted.
And lastly: some special gamer mouse drivers allow to invert the mouse y-axis. If you use something like that, please check whether you maybe have selected that option in your mouse driver.