Hello - Up until approximately 1 month ago I was able to add rest-secured services to our ArcGIS Online Portal AND be given the option to store credentials. It appears as of at least yesterday 4/20/2016 that this is not an option, or rather the option does not present itself when adding the item.
This suggests to me that our AGOL portal is not recognizing the service as secure at upload time.
WebAdaptor ssl signed by COMODO CA, Signature Algorithm: sha256WithRSAEncryption
SSL Checker indicates all hops are good, everything resolves corrrectly in the chain.