I know I'm chiming in a bit late on this, but I'm experiencing the exact same issue with my JVC KW-R500. As with the OP, I'm positive that the RCA's are connected to the rear/sub output. I turn on the high pass filter and my subs stop working (well, they stop putting out sound). I was "relieved" to see someone else with a JVC HU is having the problem. That means I'm not going nuts.
Anyhow, if the OP sees this, I'm curious as to how your situation turned out?
Obviously JVC is having this issue on more than one model. Not good. I'll be replacing this mediocre HU relatively soonish for a different brand but I'm curious about what JVC told you if you contacted them. (My HU also seems to have weak RCA voltage, but that's a whole other topic.)