AHCI, the preferred, and IDE are Hard Drive controllers. UEFI is a Bios version used on newer systems.
Secure Boot is a Windows 8-10 thing that tries to protect your system during the boot phase. Secure Boot needs a UEFI system to work.
Secondary drives are not involved in this type of thing except for which controller they use. Since there was another cumulative update yesterday I suppose you system did not benefit from it..
When you connect the drives through a USB port, what type of device are they running on? Possibly that device has them set in a specific configuration which Windows is having a hard time with..