OK, that explains the issue. Simply, if it's a room scale domain it'll take several seconds for the CO2 from the source to mix with the rest of the flow. Similarly the CO2 will be diluted from below as fresh(er) air enters the space.
A simple check for how long you need to run is a few times the plug flow time for the domain. Ie in an ideal situation how long does the supply flow take to fill the room, then run for a few times that.
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