It is worth thinking about a sample rate mismatch, but the math does not exactly work out for that. Assuming an equal tempered scale, +4.33 cents error would equal a frequency ratio of variant pitch/ true pitch = 1.00250. The twelfth root of two raised to the 0.0433 power. The ratio of 48Ksps/44.1Ksps = 1.0884 (inverse 0.91875) consistent with a pitch variance of + or - 146.7 cents.
It is very unlikely that sampled instrument content from multiple different suppliers would have been out of tune to the same degree. It is more likely that the tuner is in error, but again if different tuners are getting the same result to this level of precision that would be very surprising. I take it that he is reading cents and not semi-tones on his tuner.
If the OP ever returns, he may fill us in on how and where in the signal chain he is measuring the intonation, whether the samples are sharp or flat according to his tuner, and whether the same instruments loaded into a different DAW are also out of tune to the same degree.