Hi,
PS configuration on the Vivado design (the resulting XSA), FSBL, PMU, ATF, uboot, linux ...all work thogether.
Where did you get your SATA reference CLK? Did you use PLL form the module or external ref from a carrier? In this case you use module FSBL, you must also initilise PLL, see FSBL code of our starterkit reference design.
br
John