@liquidgordon1 - Out of interest are you using Perforce/Version control?
Someone suggested to me that this problem may be something to do with the version control making some files read-only. I have started a new project with no version control (yet) and so far it seems to be working, adding actions to the original project config (so far) - But I have had to abandon my previous project and start afresh as any new input configs I made would stop working/corrupt over and over. I spent weeks trying to solve it.
The motion controllers would also lose their orientation when the input config stopped working as well (they would appear 90 degrees rotated) - only returning to the original (untouched) template input config would get it working and lined up again - which is odd as the input config has no orientation data for the controllers as far as I know.
@VictorLerp - my project is too big to send you as requested (14gb) - I assume this is too big?