I hit an issue like that using an add-in sata3 card. Same symptoms -- if I pluggde a drive in the add-in card then the boot drive disappeared. If I pull the add-in card disk the boot drive re-appeared. Fix was a bios update to the add-in card.
NEt +1 for trying to update the firmware on MB and drive.
Also, it sounds as though the new SSD never really worked well (fail copying, etc). SSDs seem to have a high DOA rate and/or some incompatibility issues (caused me to return a SF1200 drive and get intel 320). See if you can download a bootable disk diagnostic from the maker of your bigger SSD and see if the SSD checks out OK.