Answer: Unfortunately, based on your description I am unable to identify the pest, although it might be flea beetle. I would suggest you contact your county extension for a definite identification of the pest and their suggestions for how to control them.
You might also consider removing all of the existing soil in the boxes at the end of the season next fall and then replacing all of the soil next spring. This might eliminate the overwintering opportunity and reduce chances of their presence the next year.
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