Hi Chris,
There was a similar issue a short time ago by another Flow hive user, Cedar got involved and offered an explanation, see the post below. You may or may not be having the same problem, it just maybe that the bees have not sealed the Flow cells with adequate wax.
http://forum.honeyflow.com/t/honey-leaking-into-trough-while-frame-appears-to-be-in-closed-position/4064
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