I might throw in some info that I find looking at the 1990 model as Winnebago does keep things for a long time if they find they work!
I suspect there is some confusion on which batteries are doing what as I see this drawing looks very much like the models going clear up to around 2010 or after.
Looking at this diagram of a 1990 model which is as old as online goes:
https://www.winnebago.com/Files/File...990/089949.pdf
Top center of first sheet shows the mode solenoid and at right top is the way the batteries were built. I see the normal two 12 volt batteries used for coach things and one 12 volt used for starting. On this RV the second coach battery was an option!
Two on left are 12 volt wired in parallel with one on right used for chassis/ starting. Each set has a cable to the solenoid with a control wire LR used to operate the solenoid to connect two groups together. This is the way many, many Winnebago were built for decades!
Click this drawing of the 1990 model to get a better view or go direct to get the bigger story?
My first point to question would be what makes you think the coach batteries are starting the engine? Not saying you are wrong as I'm not where I can see near as well as you but it should not be that way, so first we need to get what is actually happening cleared up.
Being aware that folks change things over the year, it looks like this second coach battery was an option when new, so it is quite possible, somebody changed out one 12 volt that came without the second battery option and added two 6 volt in place of their one 12 volt? Not the best use of space if yu have space for two 12 volt but then there are reasons for folks doing strange things at times.
But then take a look to see if this matches any of what you have and we can sort it better.