The color of the stage icon is being driven by the "Schedule Status" filed in this environment. The field is updated based on the last status report on each project, which is then read by a custom process, which then updates the Schedule Status field. The proejcts where this issue occurred had no value in the Schedule Status field, thus the icon had no color shown on it. This was caused by a status report not being set to final, and not having actual status values set on it.
To prevent this from happening, due to the way this is configured in this specific environment. all status reports need to be set to final, and have proper status values set on them so when the process and job is run, the Schedule Status field is populated, and the proper color is applied to the stage icon.