I really enjoy having proper beekeeping with this mod(I only have my first Super, but will probably have another soon) but I have the same issue with bees not seeing flowers, despite my skeps seeing them just fine, they're even swarming which I assume means the vanilla bees are completely awake. I tried all kinds of flowers other than what I already have. It seems the modded bees are more particular about the temperature than normal skeps, as they eventually caught up to the skep bees and saw the flowers around them.
So it also seems to go back to 0 for a while after re-assembling the hive after a harvest(skeps notice flowers instantly after placed). Seems the hive is just delayed on noticing flowers for a while?
I look forward to the updated version(eventually) to see what your upgraded skills can make of it in any case.