It's possible that neither is right.
First, be sure you calibrated the refractometer with a salinity standard, either a seawater mimic or a solution specifically for refractive index measurement.
For various reasons, calibrating a refractometer with freshwater can produce incorrect results. If you did not calibrate the refractometer with a salinity standard, I would do so. This could be the source of the discrepancy. Also be sure that you calibrate the Pinpoint meter with a solution designed for conductivity measurement. A solution designed specifically for refractive index may not produce the same results when measuring using conductivity. Additionally, when measuring with the Pinpoint meter, try taking a cup of water from the aquarium and measure from that. Be sure to swirl the probe around in the cup to remove any bubbles, and give the unit 3 - 5 minutes to compensate for temperature. This will rule out any possibility of stray voltage in your tank affecting your results.
If the discrepancy still exists after calibrating with the proper salinity standards, then there is likely an issue with one or both of the standards. I would purchase a new salinity standard for the conductivity meter and the refractometer, then repeat the tests. A simple and cheap alternative to buying new calibration fluids would be making
Randy's homemade salinity standards. Be sure to note that you need a different recipe for your refractometer and your conductivity meter.
For what it's worth, I also have the Pinpoint Salinity Meter. I also have a refractometer as a backup. I used the
Aquacraft calibration fluid from BRS to calibrate my refractometer. To calibrate my Pinpoint meter, I used the standard that came with my unit. When I measure my tank's water, my Pinpoint meter reads dead on at 53.0 mS and my refractometer reads dead on at 35ppt salinity.