Colour by conservation autoenabled for colour by PID and option not ticked in menu

Issue reported by Klara Briknarova:
0. Ensure in Colours preferences that no colourshemes are enabled by default
1. Import example alignment fasta file
2. Select colour by percent identity.
3. Note different shading is applied to columns 124 and 125. These have identical consensus but different conservation scores.

These columns should be shaded identically, but in 2.10 the shading is different. Enabling colour by conservation and adjusting the slider to 0 makes the shading identical.