The 'Advanced Colors' feature was added to Home Inspector Pro version 3.4.5. You will need to update to this version or later to use this new feature.
Comments specified using the "Red" button on the damage panels will appear in the 'Report Summary' of the report. Items marked as "Black" are not going to appear in the report summary.
To change the colors, go to Report Settings > Formatting. For items marked as "Black", this is the 'Normal Damage Font'. For the "Red" items, this is the 'Serious Damage Font'. For the selection panels, this is the 'Selection/Materials Font'.
If you would like additional colors, go to the 'Advanced Color Options' tab and check the box for 'Enable Advanced Colors'. You can then specify the colors that will be available when editing a given comment on the left side of a damage panel (the "library" of comments). These colors will be available as a drop-down of the available colors at the top of the comment editor. The Advanced Colors are meant as an override over the default set in the above settings.
Make sure to save your template to make these settings permanent for future inspections.