When we flash the Thunderbolt firmware, it puts the controller in "OS Managed Mode" instead of "Internal Connection Manager" (ICM) mode. Windows and Linux require ICM. MacOS works with both ICM and OS Managed Mode, but OS Managed Mode allows macOS to provide extra Thunderbolt functionality (such as Thunderbolt Bus).
This is why the Thunderbolt Firmware Repository states:
After flashing, Thunderbolt may not work fully under Windows and Linux.
View attachment 494440
So let's focus only on the macOS issues:
- Please run IORegistryExplorer and select File --> Save As..., then post the saved file.
- Also, Thunderbolt Security in BIOS must be set to No Security.