I am running Photo Mechanic version 5.0, build 13217 and I run Mac OS X 10.8.1 on my Intel-based Mac
This should help you recreate the problem,
If you open up an image using the i button, update the iptc data and then select the command button and a number to set the colour, or just set it via the colour class bar, then save using the save and move forward button, the color class does not save.
The color class save if you don't update the iptc data, but doesn't if you do.
It worked in v4, as it was part of my workflow to identify images with updated iptc data.