My logistical sorter will not paint unsorted items the default colour, (dark blue in my setup) and send them to my empty ender chest connected to a dark blue logistical transporter. Sorted ores etc are working correctly and being painted their relevant colours, it's just the default that isn't working.

I am playing with the Resonant Rise mod pack version 2.8.7.5 which has MEKANISM-6.0.5.46

Yes, this is a known bug. I actually just ran into this on my private 1.6.4 server.

It was fixed quite some time ago for v7 which will be out soon.

Any idea what was done to fix this?