It is reproducible - this is specifically how:
User Interface – Custom Colors Recalling Preferences Presets:
When custom colors are set, such as for (ALL these settings) Project Area Background, Editor Area background & Ruler Background, then Stored as a Custom Color Preference Preset, (re-call some other preset so you can test the custom color preset function.) then when that Custom Color Preference Preset is re-selected to recall it, the custom colors are correctly instantiated BUT the “status” field reverts to display AUTO when it SHOULD display as USER. The user will not be able to know that the present color is a USER custom color and may think that the saved color was correctly re-instantiated.
Select a preset by clicking menu: Edit – Preferences… and then clicking to select a Preference Preset from the saved presets. Then click Apply and OK to Close the presets popup – now reopen to view what was just set, by clicking menu “Edit – Preferences… and you will see that no preset is displayed as selected where the preset that the user just selected should be displayed but is not.
Also Preferences are not restored when projects are reopened after preferences were selected in this project. Every time upon re-opening a project that had selected a preference preset it will always need to have the Preferences Preset re-selected in the saved presets in preferences – and when this happens the preferences settings that were in effect when the project was saved and closed are not in effect when the project is reopened. The user must always re-select their desired Preferences Preset when ever they re-open a project.
However I was not able to reproduce the colorization issues of the OP. (with 10.5.12)