For some time ago I upgraded my PC with a Crucial SSD. I put the OS on the SSD and document etc on the hard drive ALL on SATA
When my PC starts up windows does not see the hard drives anymore. When switch to hybernate and on again the harddrives come up and can be used.
If the harddrives are not up I hear a click as if the system is trying to startup the dirves once every 2 a 3 seconds.
Did you check and make sure the SATA and/or power cables to the drives didn't come lose, or pop off completely? I had the same problem recently in a new build and it was because one of the power cables came lose.