Do you have any other evidence that it is CO2, or just the tune report ?
If the report simply looks at mass 44, you could have something else such as acetaldehyde. In manual tune, scan from 29 to 100 with the cal valve closed. If it is CO2 you won't see a large mass 29.
If you do see a large 29 in addition to 44, turn the source temp down to 100 C and keep the scan going. What happens to 29 and 44 at lower source temperatures ?
Is your source an HES ?
Graphite/vespel ferrules/seals will out gas 44 for a while after installation.
I would suggest you set the transferline, source, and quad to 100, every other heated zone to off, save the method as ...oh, "prep to vent.M", then vent the MS, install the blanking gasket at the end of the column, and pump it down again. When it starts up it will only load the 100/100/100/off parameters. Let it pump at least one hour and then check again.