Basically, we are talking about two different institutions with very little legal continuity between them.

The viking-and-medieval era form of slavery, sometimes called thralldom, was indeed abolished during the 1200's. However, this was not a ban of slavery per se, much less the slave trade, rather it was an edict that all christian children born would be emancipated.

Once the 1600's rolls around and the slave trade becomes relevant, the older ban was simply largely forgotten, partially becuase swedish involvement in the slave trade tended to take place outside of Sweden proper (very few, if any, slaves were ever imported to Sweden, though swedish keels were involved in selling slaves to other colonies, although the numbers are relatively small, largely because the colonial powers tried to keep the trade insofar as possible under their own control) when Sweden acquired St. Barthelemy in the 18th century the government largely kept the existing french laws, with various additions over time.

It should note that this weird double-standard was not unique to Sweden: There were serious legal questions in several european countries over whether or not slavery was actually legal in the homeland (as opposed to in the colonies)