[HELP] MSI Z790 ACE + Apple Pro Display XDR: Thunderbolt 3 USB/HID issues on Cold Boot when RAM > 4800MHz.

Hi everyone,

I’m facing a very specific and frustrating issue with my Thunderbolt 3 setup and I’m looking for expert insights.

The Setup:

• Motherboard: MSI MEG Z790 ACE (Latest BIOS: 7D86v1G / ME FW v16.1.40.2765).
• CPU: Intel Core i9-13900KS.
• GPU: NVIDIA RTX 5090 (connected via DP-In cables to the motherboard).
• Monitor: Apple Pro Display XDR (connected via Thunderbolt port on motherboard).
• RAM: 2x 35GB Corsair Dominator Platinum DDR5 5600MHz.
• OS: Windows 11 Pro.

The Problem: I am experiencing a "Cold Boot" issue where the monitor's USB Hub and HID controllers are NOT recognized by Windows 11.

• The video signal works perfectly (I have image).
• The USB devices connected to the monitor (Keyboard/Mouse) do not work.
• In Device Manager, my monitor's USB Hub and HID controllers are not listed.
• In the Intel Thunderbolt Control Center, my monitor is listed as "Not Connected", and "PCie Tunnelling" as "Disabled".

The Twist:

• At 4800MHz (JEDEC): Everything works perfectly on every Cold Boot.
• At 5600MHz (XMP or Manual): USB/HID fails on Cold Boot.
• On REBOOT (Warm Boot): Everything works perfectly, even at 5600MHz.

Here are a few screenshots to demonstrate this, comparing 5600 MHz RAM (or XMP) during a cold boot, vs. 4800 MHz RAM or a reboot :

• Before Reboot with RAM at 5600MHz (or XMP enabled) : Thunderbolt Control Center Details :

• After Reboot with RAM at 5600MHz (or XMP enabled), or on Cold Boot with RAM at 4800MHz (XMP Disabled) : Thunderbolt Control Center Details :

• Before Reboot with RAM at 5600MHz (or XMP enabled) : Thunderbolt Control Center showing device "Not Connected" - Devices Manager is not listing USB bus and HID of the device :

• After Reboot with RAM at 5600MHz (or XMP enabled) or on Cold Boot with RAM at 4800MHz (XMP Disabled) : Thunderbolt Control Center showing device "Connected" - Devices Manager is listing USB bus and HID of the device :

What I’ve already tried:

• BIOS Settings: Disabled "Fast Boot", Disabled "ErP Ready", Disabled "RTD3", Disabled PCI "Native ASPM" and PCIe "Native Power Management", "Memory Fast Boot" on "Auto" or "Enabled", Disabling Memory "SA GV", Changing SA and DRAM voltages...
  • Settings > Advanced > Intel Thunderbolt :
  • PCIE Tunneling over USB4 = Enabled.
  • Discrete Thunderbolt Support = Enabled.
  • Wake From Thunderbolt Devices = Enabled.
  • Discrete Thunderbolt Configuration :
  • Thunderbolt Boot Support = Enabled.
  • GPIO filter = Enabled.
  • DTBT Go2Sx Command = Enabled.
  • Windows 10 Thunderbolt support = Enabled + RTD3.
  • > DTBT Controller 0 Configuration :
  • (Here Also I've already tried to add some memory space).
• Thunderbolt Config: "Discrete Thunderbolt Support" Enabled, "PCIE Tunneling over USB4" Enabled.
• Power/Voltage: Tried VCCSA to 1.20V/1.25V/1.30V...
• Windows: Updated all drivers, Intel ME, and tried pnputil /scan-devices (does nothing if the controller missed the handshake).
  • Disabled "Windows Fast Startup".
  • Device Manager → Thunderbolt Controller → Power Management → Uncheck “Allow the computer to turn off this device to save power”.
• MSI Support: They just say they can't reproduce the bug and they have no feedbacks from other users with similar problem.

My Theory: It seems like at 5600MHz, there is some kind of memory stability or memory training issue during cold boot, that creates a slight delay or timing shift in the PCIe/Thunderbolt initialization. But I don't really know...

Any help or suggestions would be greatly appreciated!

Thank you.