Eric,
Backup is aalways a good idea, I have ran this Utility and I beleive I had an issue similar to yours. That said I have had to use it for 4.4.7 and 4.5.2 when the when the tiers were randomly OVERDIST because if a conversion issue. That was the last Utility to run after you ran File|Run, *utl which there is a Utility to run a Balancing Utility for Cost, I think 4.4.7 and higher. Does you Valauation, Valauation by Period and Trial Balance all reflect the same issue?