Do you have a hangar in your ship?!
You'll want to read this blog, which has important info like: "All special bays on ships that are not your main cargo will now behave like your main cargo when it comes to ship scanners and loot drop chances" and "Blockade Runners are being updated to be immune to cargo scanners, and as such will always show up as empty on scans"
EVE Online Dev Blog: Corp Hangars on Ships and You
community.eveonline.com
So, we're changing Corp Hangars on ships in Retribution.