Eric
Thanks for the data - if I run a Surface to Surface Report in 5.21 I am getting 39.7 yd3 between the two surfaces. If I constrain it to a rectangle boundary around the area where the differences are I get the same result so I am not sure where you are getting thenumbers you are showing.
The Isopach in the file you sent me - if you look at its properties, it shows the following (without me touching anything

The volume is 40.8yd3
Maybe you are reading the Area of Cut and Area of Fill values to get your 4000 number?
The area of the Cut and Fill is ~20' x 32' ie ~600 ft2 - however I assume that over the entire site there are some areas where the Cut or Fill is not 0 but 0.01 or something above our zero cut fill tolerance, which is why these as/reas are not 600 ish, but despite that the volumes look right to me.
I am comparing the Surfaces that are in your Isopach ARCH SG 200313 (Initial) and 19248 SG 200416 - these appear to be what you are computing from.
I am running v5.21 of TBC - It may be a Version issue possible - so I would need to know what version you are looking at to go any further here - I left you a VM to call me back on +1 720 323 0481 so we could chat through it in case I am missing something here.
Alan