you can see a video here.
https://www.youtube.com/watch?v=oSTVqBp_368&google_comment_id=z13tjvhblv3bipn3423tszmwyk3ytji1e

comments on the video do a good job of describing the issue.

Basically if you set the Villager to BUY an item from you that has custom, name, or enchantments etc. It ignores the special effects that are on that item. For example:

Villager sells enchanted Iron sword fortune 2, and is asking for enchanted iron sword fortune 1. A good deal I agree, however He will allow you to buy the sword using a plain un-enchanted iron sword. The same thing goes for a custom named object. As seen in my video.

I am guessing this is not by design.