Electrospray space propulsion thrusters often employ transformer coupled high gain dc-dc converters. These thrusters have a unique load resistance profile that can vary dramatically during operation. Transformer coupled high gain dc-dc converters working in very low power modes can enter a unique discontinuous conduction mode (DCM) caused by a coupling effect between the boost and magnetization inductors in the converter. The transformer magnetization current prevents the boost inductors from discharging properly, which causes premature loss of boost action and higher than expected boost inductor voltages. This mechanism generates abnormally high voltages on the converter's output side, leading to converter and thruster failure. Parameter sweep simulations show that once the converter's load resistance range is known, this DCM can be prevented or have its effects minimized by increasing the transformer magnetization inductance, the boost inductance, and the converter operating frequency. The voltage waveform across the transformer's primary winding can be actively monitored for the presence of this DCM, and the converter's operating frequency and duty cycle can be dynamically modified to ensure the converter remains in continuous conduction mode (CCM).