I went into the menu, before accepting a cryptarch package from leveling up, to equip a higher light level helmet. After I equipped the helmet, I exited the menu. The cryptarch no longer offered me a package. She just wanted to take my house banners. This was at the iron temple and I had house banners to turn in. I bet it has something to do with switching the house banner turn in, from the beginning to the end of conversations with the cryptarch.