from time to time, there where reports about unexpected frequency offsets with the Pluto. I am not sure but my recommendation is, bring all calibration settings in the Console to zero. Use all the options that are shown. Probably in the Plutos firmware are factory offsets.
This happend to me using the pluto not for satellite operation but on 2m and 70cm. Returning to Sat-mode I found a strange offset altoughan external Leo Bodnar Clock is applied. After a cold start all was fine again.
Yout settings of the environmental variables above seem to be ok.