I'm not sure if it's the line-in jack problem, my R-09 is only 2 months old and I had the same problem when using the preamp with my R-1. Also, the HPF switch is set firmly to off...
The gear was being moved around a bit, but I did check the connections and they were tightly in, so I'll have a look at the cables, especially the one that connects the R-09 and the CA-9100. Thanks for the replies everyone!