I was able to verify that the down-binners do work correctly when upgraded in quality.
Given the number of mods in your save I don't think it's possible to figure out what might be causing the issue, since by every other long-running game it seems to work fine.
But, to potentially make it more robust, I did add automatic rebuild of the list of placed down-binners on configuration change, which will hopefully make it more robust. And, I've added quality-down-binning-rebuild as a command to force a rebuild if it happens anyway. Implemented in 0.8.3.