I am desperately attempting to understand your problem.
I usually prefer to calibrate my bombsight at full throttle.
Before that point, though, I level off and accelerate until my E6B climb indicates "3", then I open my bomb bay. That has the effect of bringing my climb to zero, or at least really close.
With the E6B climb indicator reading zero, I calibrate. Usually I am right on with my calibration speed matching my true airspeed. Occasionally it might be one mph off, but it still works.
The other thing I pay attention to is my actual altitude versus my drop altitude. Any blatent differences and you might want to recalibrate.