As a follow up to this investigation. I have been able to reproduce the issue using the sample file provided.
With an older ImageJ version the file opens by default with each channel displaying a separate colour. Replacing the Bio-Formats jars with more recent releases produces the same behaviour (version used was 1.51h from 30 May 2017 FIJI, final Java 6 version)
With a later ImageJ version (1.51n) the QA file opens with the same colour in each channel. Replacing the Bio-Formats version with previous versions does not affect the behaviour. Changing the colour mode in the Bio-Formats importer to Colourised does however display the correct colours for each channel.
This issue appears to be a change in how the default colour mode is handled between the Java6 FIJI and Java8 FIJI. I have opened a Trello card to further investigate if any changes are required in the Bio-Formats plugin to the default behaviour.
https://trello.com/c/8BQ2ViRo/212-fiji- ... olour-mode