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As it turns out, this issue was not caused by the labels, but rather by the size of the dataset. I was using a rather small dataset for development purposes. Not only was this dataset quite small, but also heavily imbalanced, with a lot more "O" labels than the other labels. Fixing this by using a dataset of 10x the original size (in terms of sentences), I am able to get meaningful results, even for my custom labels.

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Answer selected by mwunderlich
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