Your coach batteries are probably 12 volt marine batteries wired in parallel, but may be 6 volt batteries wired in series. In either case there is probably no way for the converter to sense a difference between the 2 batteries. All it sees is the one 12 volt source. If you can tell us the make/model of the converter we can probably tell you if it is a smart converter that adjusts to the battery state of charge. The OEM converter almost certainly did not.
The coach batteries are probably connected to the chassis battery when the ignition is on. A smaller wire is probably used that reduces the charging voltage so the coach batteries will be charged at a slower rate than the chassis battery.