Try Development Release 3.1.16(d), now available at htrtp://stuff4fs.com. (I had omitted a key element from the earlier fix.) The earlier fix reported no parking available at the add-on airport and, hence, the Analyse Parking button being disabled when Add-on was checked. I am unable to reproduce that situation with Stock checked. If that situation persists on your system, then perhaps you should have a close look at the stock airport in ADE. Perhaps it's been modified.
Having looked at your files in detail, I can certainly see why the permitted number of aprons were exceeded. Unusual treatment.
Don