Two thoughts...
1) The two tables aren't quite co-planer. I suspect your infeed table maybe out of square in relation to the fence.
2) The board itself may be warped, and will take multiple passes to get that face flat. If the board was already wedge shape, the jointer can potentially make that more pronounced. Remember the job of the jointer is to make a face flat, not necessarily to keep two faces parallel. Make sure you are not putting too much downward pressure on the board when passing through the jointer. There should be just enough pressure to push the board through the knives.
1) The two tables aren't quite co-planer. I suspect your infeed table maybe out of square in relation to the fence.
2) The board itself may be warped, and will take multiple passes to get that face flat. If the board was already wedge shape, the jointer can potentially make that more pronounced. Remember the job of the jointer is to make a face flat, not necessarily to keep two faces parallel. Make sure you are not putting too much downward pressure on the board when passing through the jointer. There should be just enough pressure to push the board through the knives.