I've been watching this question for a few days now and decided that today I would hazard a Wikipedia-fueled attempt at finding a plausible answer. Here goes...
The word "Catholic" in reference to a specific organization seemed to be originally used to distinguish the Church of God from the churches of heretics. The earliest form of this use I found was from the Catechetical Lectures of Saint Cyril of Jerusalem, which he delivered around 350 A.D. He says:
- But since the word Ecclesia is applied to different things (as also it is written of the multitude in the theatre of the Ephesians, And when he had thus spoken, he dismissed the Assembly Acts 19:14), and since one might properly and truly say that there is a Church of evil doers, I mean the meetings of the heretics, the Marcionists and Manichees, and the rest, for this cause the Faith has securely delivered to you now the Article, And in one Holy Catholic Church; that you may avoid their wretched meetings, and ever abide with the Holy Church Catholic in which you were regenerated.
Now, the use of the word "catholic" here can still technically be translated as "universal" given that the churches he referenced followed heretical teachings and are suggested in this passage to not have been regarded as true organizations with the mission of following Christ. However, the word is still making a clear distinction between two groups here.
Another instance of the word "Catholic" being used in a distinguishing fashion is in the Edict of Thessalonica, published during the reign of Emperor Theodosius I:
We authorize the followers of this law to assume the title of Catholic Christians; but as for the others, since, in our judgment they are foolish madmen, we decree that they shall be branded with the ignominious name of heretics, and shall not presume to give to their conventicles the name of churches.
Here is probably the most blatant use of "Catholic" as a proper noun per se, as the word "title" is specifically used to define a "Catholic Christian."
In conclusion, it seems that the word "Catholic" was originally used as a proper noun to distinguish the original Church from heretical sects. Technically, I as a Protestant am a heretic in the Catholic understanding, so such a usage is still accurate in that sense and conveys similar meaning.
Catechetical Lecture from New Advent
Edict of Thessalonica translation