I spent all day at this yesterday but my brain is fried.
My desktop started experiencing this issue recently where it would boot to the Windows black screen with the spinning dots and just sit there.
After messing around yesterday - I found out that this issue doesn't happen when I disconnect my second harddrive.
I have windows on a 128GB SSD (Samsung SSD 840 EVO 120GB) and an extra 1TB HDD (Western Digital WD Caviar Blue 1TB) - I install everything to the HDD, App, documents, downloads, photos etc.
After much connecting / disconnecting - I manged to get to the startup repair screen.
After a long time - it said it couldn't repair my pc.
I decided to wipe windows and install again.
Once installed - same issue was happening. I eventually managed to get into windows with the HDD disconnected. I then managed to log in with the HDD connected - it wasn't usable (errors like "the parameter is incorrect", unable to format etc.).
I used WD Data lifeguard software to wipe the HDD. Windows could then see the drive and use it without any issue. I ran chkdisk and checked the smart values and everything seemed okay.
I've restarted my pc and the issue is back. Refuses to boot with the HDD connected but fine without it.
I've tried using a bootable copy of windows 10 to repair but nothing seems to work.