Yes, it is a known limitation that the sample tuner doesn't always work reliably. Possible workarounds that work for some but not all samples are documted in the manual.

You could do like the sample-tuner in the soundfont-editor Polyphone and play a reference tone at 440 Hz at the same time as the sample and tune it until the oscillation stops or almost stops.
Works in 99% of the cases, works well for finetuning, although a bit unpleasant for the ears so keep the volume low.