What laptop do you have? Does the hdd show up like this sporadically too? Did you make sure to connect all cables back in the right places? Sounds like a faulty drive or motherboard issue if both drives appear sometimes.
The HDD always appears in the BIOS. I think I'll try switching the SSD to that port.
My laptop is an ASUS G51J-A1 and I have put in a Samsung 830.
Make sure your mobo is in ahci and that it supports sata3 too.
Switching the port solved the problem.
Could have been that it was plugged into a sata 2 port. Glad you got it working now.
same problem, i can tell you we did nothing wrong, the problem is either on windows (hopefully) or on the BIOS