I use the variable aperture option often and haven't seen a problem. We'd need an example set of a few images you are using and a backup of your preferences file (Multi-plot Main > File (near the bottom)) to see if we can duplicate what you are seeing.
I ran a stack of 10 images using your AIJ_Prefs file and I get a valid relative flux for each image (see below). I noticed that auto comp stars is not turned on. Are you manually selecting a comp star? I selected one manually for my run. Other than that, I made no changes to your set up.
Or is this only happening when running from a Macro? If so, can you check outside the macro environment to see if the problem still shows when you run AIJ interactively?
I typically pick my comp stars manually. I'm seeing the failure as I go through the DP. After I select my target and comps with variable apertures selected, the differential photometry starts but no values are written in the measurement file for the relative flux. Let me see if can provide additional info.