a. that estimated file size is just the file size of the raw video stream
b. depending on the source it might fluctuate a lot
So let's see what is happening.
using the frame count that Hybrid assumes the output should be it calculates the probable output file size based on those values.
(not taking any container overhead or other streams into account)
In case that estimation is off a lot it is probably because:
Hybrid assumes the wrong number of output frames
(sounds like some bobbing is done and Hybrid doesn't account for it during the output frame count estimation,...)
x264 reports wrong values
the x264 output format changed (this can happen if modded x264 builds are used or the official output format changes)
since I haven't touched that code for quite some time my guess is that Hybrid assumes the wrong number of output frames.
Just encoded 4 movie sized clips and the estimated file size shows the proper values, so my guess is that some setting you choose let's Hybrid assume a wrong output frame count.
=> not enough details for me to do more than trying to blindly reproduce the issue which I did and here the estimated output size behaves as estimated.