A student pointed out on the course discussion board that I'd not used colours consistently in drawing chromosomes. I apologized for the confusion and tried to clarify it in a response.
But then I raised the issue directly in class yesterday, pointing out that on Monday I'd coloured the two chromatids in a pair differently (dark ad light blue), but on Wednesday I'd coloured them the same shade of blue but coloured their homologs pink. And the transparent strips I used to demonstrate meiosis had the three different chromosomes from one parent green, whereas those from the other parent were blue.
And I then told them that I was about to use yet a different colour coding in yesterday's class, with the homologs the same colour (maternal distinguished from paternal by a wavy line drawn on them) and the different chromosomes (those with completely different genes) different colours.
The class had been given strips of coloured paper to use as their won chromosomes in solving our first genetics problems, and I told them to pay attention to the colours they used, with the goal of having the colours a guide to the relationships between the chromosomes they were representing rather than a source of confusion.
The most important thing isn't that they get the colours right, but that they learn to think about what colours will be least confusing, and more generally about how to represent the factors that matter in any given problem. It's this thinking that leads to the most learning.