With some assistance from Fortinet technical support, we eventually found the cause of the " missing data" in the PCI Wireless report.
After the upgrade to v5.0.7 (and possibly even earlier, the upgrades to 4.3.14 and 4.3.15), the GUI for the FG200B was showing correctly that we had " Accepted" certain WiFi APs that had been detected in/around our environment ... but despite the GUI showing this, the data being delivered from the FG200B to the FL100C was NOT correct ... and so the FL100C could not report on it properly.
We had to note down all the Accepted APs, mark them as Unclassified, and then re-mark them as Accepted again in the FG200B.
After that was done, the correct data was again flowing to the FL100C and the report has data in it again.