Hey there, Archillect.
Did you by any chance disconnect the drive during the Windows installation process? This is recommended in order to avoid future issues.
If you used to have the HDD as a main drive up until now, I'd recommend that you disconnect the SSD, to see if you'd be able to boot to Windows via your hard drive. If that doesn't help, check if it's recognized at least by the BIOS/UEFI.
You should also give it a try with a different SATA port and cables, or even better - with a different computer, to see if it's recognized.
Hope that helps. Please let me know how everything goes.
Boogieman_WD