Best Bike Split obviously uses a ton of variables; if any of them are significantly off it can have a huge impact on the predicted time.
Couple of things come to mind:
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Did you run your power file back through Aero Analyzer to get an updated CdA (sounds like you did when you said you “put it back into BBS for analysis”)?
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Did you update your weight (with kit and all equipment), loaded bike weight (including nutrition and spares), component type, etc in the “My Bikes” tab? My understanding is that BBS uses the mechanical loss component from that page regardless of what you put as CdA.
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Your CRR seems unrealistically low. Depending on tire and road conditions it could easily be double what you have input.
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BBS produces an estimate based on an optimal pacing strategy. It seems like you unfortunately had to wing it based on the cue sheet so I imagine your pacing strategy was not exactly the same as what BBS suggested.
All that being said, it is still an estimate and modeling tool so I would still expect a difference.