tREF 0516 and 2592 are settings from the BIOS? If yes, then the option.rom should work normally.
Maybe I shoud explain how the additional settings work. The System starts with the default values in tRC, tRFC, tREF, DS, SR, alpha timings and romsips. Right before the system boot from hard drive the option.rom starts as the last module in BIOS. The option.rom reads the additional settings you set in BIOS. According to this the option.rom change the values you set before.
If you set "auto" in the additional settings, the option.rom skips the change for the active setting and jumps to the next setting.
So, if tREF is set to "0516 cycles" and boots with 0516 the option.rom should work properly. I am not sure why you get a 0016 value with a "auto" setting in BIOS. Maybe it is related to the tool?
could you make two screenshots like this one ?:
...
one after a bootup with tREF="auto" and one after you start the tool?