I would suggest that you check to make sure that "fast startup" is not turned on.  It should look like this... [IMAGE]causes more problems than it solves "I have to load the BIOs and save and exit in order for it to boot from the SSD. Once it boots the SSD still works no problem."   If the "shut off the fast startup" doesn't help, then try the procedure in the service manual for clearing the CMOS. It sounds like the BIOS is still looking for Windows on the old drive, must be nostalgic.    
I recently installed a Samsung 860 EVO 500gbs into my Alienware Aurora r7 desktop. I wanted it to  be the main boot drive and I going to wipe the old HDD and use it for storage. I cloned the HDD onto the SSD, I disconnected the HDD and confirmed that the SSD could boot to Windows no problem. I then reconnected the HDD and wiped it using the "Clean" command in DISKPART. I then reinitialized the old HDD and formatted it.  For some odd reason whenever I do a full shutdown and boot back up the Alienware SupportAssistant starts doing a scan for errors on the old HDD and I have to load the BIOs and save and exit in order for it to boot from the SSD. Once it boots the SSD still works no problem. And when I just do a restart instead of a full shutdown it boots to the SSD no problem. I'm not sure what else I can do cause I know that the old HDD has been wiped clean of Windows so don't know what else to do. Any advice would be appreciated. 
Aurora R7, issue with new SSD as Boot drive