Drive management may be more at issue than Armoury Crate.
Let's say that your Western Digital drive has no drive letter assigned, and your Segate has drive letter E.
If the computer detects the WD first, it may get drive E assigned, then when the Segate appears, it can't have the drive letter it is assigned.
I would assign drive letters to every drive, reboot and see if the issue still occurs.
I have the exact issue you have. To verify the issue I used Armory_Crate_Uninstall_Tool and my problem went away. Then used ArmoryCrateInstallTool to reinstall and problem came back. Just like you it affects my external USB drive. I noticed when booting my PC the external drive is working until the Armory Crate kicks in and turns on my LEDs it is controlling. I have a annoying temp fix I have to do, Once everything is done loading I have to unplug the external drive and plug it back in. All my drivers are all up to date. Really would like Asus to a fix this issue.
I have a annoying temp fix I have to do, Once everything is done loading I have to unplug the external drive and plug it back in. All my drivers are all up to date.
I do it the some. But this is not a convenient solution. I wrote to Asus support many times. They ask for updates of Armoury Create every time....I have this issue for over two years. Mr. Asus, do something about it. !!!