I found it fascinating that Cap found him strapped in a medical table groggy (possibly drugged). Perhaps this is one of the ways the writers will explain Winter Solider if they go that route in sequels.
This is what I'm thinking. Whatever Zola was doing didn't seem to turn Bucky into a super soldier, but It could have had other effects that would make the Winter Soldier scenario possible. In fact, it could be That Zola laid the ground work for the mind control aspect.