Hi Pat, and welcome to AikiWeb.
I don't think this type of thing happens very often, and actually, we don't know if this CI derives his/her entire living from running a dojo. It almost sounds like poor bookkeeping and accounting practices above all else, but those in his/her dojo are the ones in the know. In my 20-years in aikido, I've yet to meet up with this type of practice, and certainly cannot imagine that it happens with any frequency.
I would really like to hear how this situation is working out, but the original poster has not chimed in recently to let us all know.