Alan, I see you have a 2007 unit. According to the manufacturer you should replace the "duckbill" valves every 3 years. They have to do with pulling the vacuum, I don't know how specifically, thus if you have not replaced them that could be part of the problem. I have a 2015 Bounder 35K and replaced mine last fall, found pictures on irv2.com under waste problems. It wasn't a bad job, just flush lines clear and run some Dawn though before disconnecting the vacuum generator. Other possibilities are as others stated; toilet seal, a line somewhere or loose bolts.
I have found the system to be rather efficient though we do not put TP in the commode, put in waste can. Secondly "school" your guests on how to use the system.