Plastic speakers do resonate at different frequencies than wood boxes, however, that may not be the issue.
The smaller the low frequency driver, the less directivity at lower frequencies. So, there would be little difference between a wooden box and a plastic enclosure with regard to the directivity of the frequencies in question.
If you don't have a 31 band EQ, or parametric EQ in the signal chain, adding one will allow you to make those adjustments reducing the frequencies in question. (off the top of my head, around 150Hz)
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