Hi Julie,
I think your colony may be too small for a super (Flow) at this time. You will need to give your colony time to build up their numbers, at least 6 out of the 8 frames in the brood box should be fully drawn out and covered with bees. If not, take the Flow super off and replace with the lid & leave as a single brood box till the numbers have built up. I am assuming this is a single brood setup and not a double.
Are you seeing healthy brood i.e. eggs, larva and capped cells? Are there any perforated cells or chalky/whitish lumps within some of the cells?
You may have 1 or multiple pests or disease to contend with. Can you supply photos of the larva on the bottom board and some photos of your frames, make sure they are in focus.
The larva could be bee brood (drone or worker) that has fallen from damaged cells when the frames were removed for inspection… or it could be wax moth in which case you will see silky webbing over your frames. If its small hive beetle then the frames may be slimed. Chalky lumps may be Chalkbrood or Stonebrood, which is a fungus.
Have a read of the following post and let us know what you think, but as I said photos is what we need.
http://forum.honeyflow.com/t/bee-diseases-and-pests-a-summary/1570
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