It is hard to tell exactly what you are seeing, but the most common thing that can happen because a PRT is placed into a vacuum, is a loss of the convective path for transfer of heat. As the vacuum is drawn, the measurements become more dependent on conductive paths and to a lesser degree, radiation. There are several possibilities for a differential as a result. It could be that one PRT has a good conductive path to dissipate the measuring current and another has little conductive path and is only able to radiate the heating. It could be that the unit with poor conductive path within the bell has a good conductive path to the outside of the bell where there may be a temperature differential.
It would take more information on the parts involved and the test setup to suggest anything else.
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