An injection molding system and methods for improving performance of the same. The system includes a plunger rod and a melt zone that are provided in-line and on a vertical axis. The plunger rod is moved in a vertical direction through the melt zone to move molten material into a mold. The injection molding system can perform the melting and molding processes under a vacuum. Skull formation in molten material is reduced by providing an RF transparent sleeve in the melt zone and/or a skull trapping portion adjacent an inlet of the mold. It can also be controlled based on the melting unit. Vacuum evacuation can be reduced during part ejection by using a plunger seal, so that evacuation time between cycles is reduced.