Do the CSS selectors that the custom CSS file uses to add these color styling still exist if you inspect the RT element that is being targeted?
It could be that the class names or IDs being used in 4.0 have changed when moving to 4.2 or are not as specific as the new themes selectors and therefore are being overridden.
Does RT not provide any css from their side to color these fields
By default, RT does not color these fields based on status.
See: Customizing/Styling rt - RT 4.2.16 Documentation - Best Practical