First did you buy both modules from the Store or Steam? If the latter did you sync you Steam and Smiteworks accounts via 'manage' in settings? If you bought them from the Store did you sync your Paizo account if you claimed a discount for owning the pdf?
If the above doesn't apply can you open up your FGData folder (click the small folder icon top right of your start screen) find the vault folder and check to see if you have a module in there called PZOSMWPZO90139FG.dat (if you bought AP1) or PZOSMWPZO90140FG.dat (if you bought AP2). If you see a file there then delete it and then do an update of FG.
If you don't see the file there that you bought then something must have gone wrong with your download. If you are seeing the purchase in your purchase history then you should contact
[email protected] who can look into the matter for you.