When the system is warm, it works flawlessly. My guess is something is lose and a connection is lost when things are cold. Any thoughts on troubleshooting this. I've reset the memory and the CPU. Graphic card and LAN are on the motherboard. Is it a faulty MB, should I send it back to Shuttle?
I have had SATA ports with kinda dodgy connections, may be worth checking them really quick. I found that if I seeated them at the full depth the connection was flaky, pulling them out a fraction till it felt tight seemed to do the trick for me.
BINGO! Let the machine cool down, it wouldn't start (same symptoms as before). Opened up the case and checked both SATA cords, I noticed one of them was zip tied (Shuttle factory install) and the cord looked a little tight and pulling connector a tiny little bit to the left. Undid the zip, reattached with more room and restarted.
The machine started up properly immediately afterwards.
Will do some more testing to make sure this is it and not some other silly thing that got bumped when I was opening the cover. But looks like you solved the problem!