Same here. I have a Crucial mSATA I run the OS off of. But whatever is wrong with the controller for the 2.5" was crippling my system like crazy. For the last couple of days I've had the WD Red drive hooked up via a SATA to USB adapter and it's been running perfect like that for the last 2 days, with it constantly being on.
This is the setup that does all my automatic downloading, so it's supposed to be up 24/7, with all the downloads going to the 1TB drive. This obviously wasn't working for me though with the system just randomly deciding that it all of the sudden doesn't like the 2.5" anymore and just makes it go away. Haven't had any issues though since going to the USB port.