Well there are a couple different ways to fix this. First, picking up the engine itself would give you a quest to talk to Shiro, so if that did not proc I would delete the engine and try again. Also, deleting the engine and picking up the duplicate from Shiro may also help. Just be careful since if Shiro does not have a duplicate engine to give you, you will HAVE to redo the raid to get it. I will keep my ear to the ground for you to see if I can find another way around this bug.