I was testing the default wing in supersonic flow in VSPAERO and the values in the *.flt and *.stab files didn't make sense. For example, it was reporting the neutral point of the wing as being hundreds of length units in front of the wing. The text files also had the total lift coefficient as being somewhere around zero, or even negative. Using the viewer the results looked reasonable; it was only the text files that had the issue.
Digging in it looks like the values for "clo" are the issue. It seems like the derivatives are calculated based on the "clo" instead of total "cl" when calculating things like CL,alpha and Cm,alpha and reporting in the text files. The values for "cli" and "cl" in the results manager seem fine. It's only the values in the *.flt and *.stab for supersonic cases that seem to have the issue; all subsonic results don't have the same problem.