You have not provided enough information to answer fully:
What was your 12v system voltage?
What make and model of the two devices in question (ideally with links to their data sheets
so that I don't have to go searching)?
What peripherals do you have attached to the Pi (again make and model and links to data sheets)?
Depending on the design of you DC/DC converter the output may not be stabilised but follow the input and if it is an automotive targeted product it will be looking for 13.8V - 14.4 V on the input. Does it get warm? Do you still get the low power
warning when you are running your engine
with the alternator
putting out 13.8 - 14.4V?