grammatical number - How should we treat a plural term that refers to singular term?

I'd like to better understand why is the following grammatical:

One of the problems is flags.

Here flags refers to the flagging system. However, flags is plural and the flagging system is singular.

I would consider the following alternatives grammatical:

One of the problems is the flagging system.
^{This is the actual meaning.}
One of the problems is the flagging.
^{This would be best option if the problem is in the process of flagging.}
One of the problems is caused by the flags.
^{Best if the problem was with displaying the actual flags, but avoids the [singular] is [plural] pattern.}
One of the problems is “flags”.
^{Quoted to denote unusual usage.}

The original is semantically clear to me, but I am unsure if it is grammatically correct.

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NOTE:
This is related to the following question and this answer. There is already a short answer there, but I wanted more details and references to grammatical rules that govern this case (so I can further explore on my own) and thought it would be noise over there.

Answer

One of the problems is flags.

This is grammatical because the subject of the verb is is the singular pronoun one. Trim away the prepositional phrase and the predicate, and you get:

One... is...

... which is obviously correct.

One is very frequently used with a prepositional complement containing a plural noun, such as of the problems. This does not change the grammatical number of the subject.

One of the boys is sick.

One of the trees is falling over.

One of the candidates will win.

The only further wrinkle in this sentence is the fact that the predicate nominative flags is also plural. This, too, does not change the number of the subject, and it fact joining a singular subject with a plural predicate nominative is very common in English.

Open-source is many different developers working together freely.

A woman is not just her breasts.

So there really isn't anything ungrammatical about the original form of the sentence. Some people may find it infelicitous, and it could probably be reworded for clarity or style, but it isn't violating any of the rules of English grammar.