Back in the "old days" (ACA v4), we used to use these two columns (those currently showing as 0.00000 in your example above) to store the prior (self-explicated) utilities, and the Pairs utilities (those estimated only using the Pairs data). Then, ACA v4 used to try to estimate an "optimal" weighting of the two sets of utilities to best predict the calibration concepts.
Now, we do things differently. And, the only program that uses the .acd file is the ACA/HB estimation module. The ACA/HB module estimates utilities in a very different way, using hierarchical Bayesian analysis. But, to make sure ACA/HB software can read both new and very old .acd files, it was necessary to keep the same file structure as before. Hence, we just pad those columns with arbitrary 0s, because HB isn't going to use that information anyway to estimate the utilities.
So, this is all as expected, and you shouldn't be worried that anything is going wrong.