if had a similar problem, trying to install 1.2 Beta-2 and after the installation bootloader always kept saying: can't find kernel, until I see, that the hd was connected to the second IDE channel. So I plugged the hd into the first IDE channel and voila, after a fresh install (config backuped) pfsense starts. Maybe you have the same problem. Try to connect the harddrive to Sata1