Did you use a single or dual capillary DP transmitter? It sounds like you may have used a single diaphragm transmitter in which case the LP side is vented to atmosphere and as soon as you pressurize the vessel a high level is inevitably sensed.
For your application you would need to install a dual capillary DP transmitter with the low side on the top of the vessel and the high side at the bottom of the vessel. Then you would have to calibrate the transmitter using the specific gravity or relative density of the fluid it is measuring to ensure an accurate reading.
With the dual capillary TX the working pressure of the vessel in question is sensed equally between the LP and HP sides of the transmitter and therefore is naturally zeroed out and only the level of any fluid will be measured with the transmitter.