Two thinks come to mind:
(1) that "2800 RPMs" may be what it is rated at at Max 12 V ie 12.6V ( or even higher as one fan I looked at was rated up to 14V). What is your 12 V, may be just under 12 V ie 11.8. Who knows a half a volt may be about 300 RPMs???
(2) Believe these use a coil where the emf induced depends on the RPMs, more a question but what is the accuracy of these, 3%, 5%, or even 10% - Unknown as not often published.
Could be, and probably is, a factor of Both.
If you wanted to (Not worth it nor would I) you could make a little pigtail and run the sense and Gnd to the mother board HSF connector, and the +12 V and Gnd from the fan to an adj 12 V PS and adj between 11Vand 13 V. AS I Said is it worth it
Most are not two concerned as long as it does it job. But the ONLY way to verify RPMs would be to use an instrument designed to measure RPM's - not realistic in this case.