This bug occurs when a chunk containing a barrel with Forestry bee drones (and potentially princesses) is unloaded and reloaded.
The barrel completely deletes the IsAnalyzed tag from the drone’s NBT data. This prevents freshly created drones, which have the tag, from stacking into the barrel.
This event also occurs in GT6 hoppers.
I found this on the Bears Den GT6 Adventure modpack, if that makes any difference.