Temperature variation could play a role. Was it the same batch of bark each time? With sufficient agitation the polar/NP phases should equilibrate pretty quickly so there's no real need for the pulls to take that long, unless you were waiting for emulsions to clear.
As it looks like your yields are rounded to the nearest 50mg, is there a possibility of measurement error? What were you using for weighing? How well does it respond at lower values? Your two results are in the same ballpark, so they could be viewed as consistent enough. 0.9% is OK but not outstanding, 1% obviously a marginally better yield.
Without more detail it's hard to comment much more on your results and a sample size of N=2 isn't statistically significant. What form was the bark in? Did you process it in any way before adding the base? Was solvent re-used after freeze precipitation for any of your pulls? The extra 50mg the second time around could easily be explained if the solvent were re-used.
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― Jacques Bergier, quoting Fulcanelli