Different thing are happening to different people here.
I wanted to replace the 500GB SATA hard drive in my MacBook Pro with a 750GB disk. I hooked the 750GB up to the MacBook through an external USB - SATA interface. Formatted the 750GB disk, did a clean install of Mavericks and moved a bunch of my stuff across from the 500GB.
Could happily boot up the new system on the 750GB disk while attached to the USB - SATA interface.
Time came to swap the disks over - ie put the 750 inside the MacBook and take the 500GB out. No joy - would not boot - got the flashing Folder with question mark. Read all the stuff in here about new cables etc . Got a new cable - same problem.
Turned out to be formatting of the disk. Showed up as having one small partition when installed internally - doesn't seem to cause any problems when connected externally. Have reformatted the disk as MacOS extended journaled, 1 partition - disk now recognised. Cost me £20 for the cable and a lot of wasted time reinstalling the system all over again etc etc. But heh ho - stuff happens.
Anyone want a brand new cable......?!