I had to deal with a ThunderboltEX3 installation in the last two days and also for me it turned out to be quite a challange. I read through multiple forum posts and would like to share my experience here. It might help some other people.
ASUS ThunderboltEX3 card
Windows 7 Pro
Connect a Promise Pegasus2 R4 (via an Apple Thunderbolt3 to Thunderbolt2 adapter)
I installed the drivers (Version 18.104.22.168) from the ASUS website first (https://www.asus.com/us/Motherboard-...528.1531212571
), turned off my PC and placed the card inside my system (PCIE16x_2). Booted up once without any changes in the BIOS and shutdown again. Entered the BIOS and just enabled the Thunderbolt support and set the correct PCIE slot. Saved my changes and rebooted my machine.
After my machine was up and running again I started the Thunderbolt Software and tried to connect a standard LaCie Rugged drive to the Thunderbolt (USB-C) port. Unfortunately no success. I tried the first PCI Express (PCIE16x_1) slot in my system with the same result. The details of the Thunderbolt software showed a correct version number for the "software package version", "Application version" and "Service version" but the "Controller driver version" was Unknown, so I figured the controller is not recognized by the system. During this whole process I also updated my BIOS to the latest version 1302. This removed quite a lot of entries under the Thunderbolt Configuration and added a few new ones. Last chance, PCI Express slot 3 (PCIE16x_3). Connected the card to it, changed the slot under the Thunderbolt Configuration in the BIOS, restarted the system, waited for a few minutes after my machine was fully up and connected my LaCie to it and finally the Thunderbolt software popped up and asked if the device should be connected to the system. YEAHHH!!!!!
After this success I installed the Promise Pegasus drivers from the webside (don't really know if you need them, but I thought better be save than sorry), restarted my machine and connected the Pegasus via the Apple Thunderbolt3 to Thunderbolt2 adapter and it got recognized by the system as well. I daisy-chained another Pegasus RAID to it which also showed up.
Long story short: Make sure your BIOS is running the latest version. Install the drivers. Install the ThunderboltEX3 only in PCIE16x_3 slot. Choose the right slot in the BIOS under Thunderbolt Configuration ( I didn't change anything else in the BIOS other than the slot where the card is installed).
Be patient when connectiong your LaCie or Pegasus Raid for the first time. It took quite a while until it installed the driver and the controller got recognized by the system. A reconnect might be necessary after the first try.