Turns out the BIOS was not ready for SSD. I've yet to see a virus do this so my thought is to ask the machine's maker to tell you if SSD is supported.
There are other oddities such as iffy SATA cables, a SSD drive that needs its firmware updated, power supplies that are pushed to the edge but let's not drag that into the conversation without full details.
Have been having this weird issue where, it's as though my SSD (has Windows on) goes to sleep and I have to wake it up again. I'll sometimes get it on boot up, and annoyingly I can be half way through doing something and my PC will just shut down and when I boot it back up 'Boot MGR is missing' is on the screen.
Each time all I have to do to get back onto Windows again is turn it off, press F2 to enter Bios mode, and select to boot from the SSD.
Easy to fix, annoying when it happens. Any ideas of what is causing this? I run regular virus scans and have read that could be a cause of it but all is clear.