Hi,
I need to be sure what you are trying to extract here in this circuit? May be if you can share your file, I can look into detail. But generally, if you put the probe after the fiber, it should measure the power coming out of the fiber (in Watts). And Probe after the photodiode should give you the current as a function of voltage.
I am not sure what you mean by reverse phase? Can you share the plot image and explain what you expect? In general, if the response you are getting is reversed then may be try to put the probe before the fiber and photodiode. See if the response is what you expect.
If not, then please share the circuit file on saurabh.bedi@optiwave.com, so that we can look into details of your simulation.
Best,
Saurabh Bedi.